Synthetic ligation reassembly in directed evolution

ABSTRACT

A directed evolution process for rapid and facilitated production from a progenitor polynucleotide template, of a library of mutagenized progeny polynucleotides wherein each of the 20 naturally encoded amino acids is encoded at each original codon position. This method, termed site-saturation mutagenesis, or simply saturation mutagenesis, is preferably based on the use of the degenerate N,N,G/T sequence. Also, a method of non-stochastically producing a library of chimeric nucleic acid molecules having an overall assembly order that is chosen by design. Accordingly, a set of progenitor templates, such as genes (e.g. a family of esterase genes) or genes pathways (e.g. encoding antibiotics) can be shuffled to generate a sizable library of distinct progeny polynucleotide molecules (e.g. 10 100 ) and correspondingly encoded polypeptides.

RELATED APPLICATIONS

The present application is a continuation of U.S. application Ser. No.11/798,032, filed on May 9, 2007; which is a re-issue of U.S.application Ser. No. 09/594,459, filed Jun. 14, 2000 (now U.S. Pat. No.6,605,449); which is a continuation-in-part of U.S. application Ser. No.09/332,835, filed on Jun. 14, 1999 (now U.S. Pat. No. 6,537,776), whichis hereby incorporated by reference.

FIELD OF THE INVENTION

This invention relates to the field of protein engineering.Specifically, this invention relates to a directed evolution method forpreparing a polynucleotide encoding a polypeptide. More specifically,this invention relates to a method of using mutagenesis to generate anovel polynucleotide encoding a novel polypeptide, which novelpolypeptide is itself an improved biological molecule &/or contributesto the generation of another improved biological molecule. Morespecifically still, this invention relates to a method of performingboth non-stochastic polynucleotide chimerization and non-stochasticsite-directed point mutagenesis.

Thus, in one aspect, this invention relates to a method of generating aprogeny set of chimeric polynucleotide(s) by means that are syntheticand non-stochastic, and where the design of the progenypolynucleotide(s) is derived by analysis of a parental set ofpolynucleotides &/or of the polypeptides correspondingly encoded by theparental polynucleotides. In another aspect this invention relates to amethod of performing site-directed mutagenesis using means that areexhaustive, systematic, and non-stochastic.

Furthermore this invention relates to a step of selecting from among agenerated set of progeny molecules a subset comprised of particularlydesirable species, including by a process termed end-selection, whichsubset may then be screened further. This invention also relates to thestep of screening a set of polynucleotides for the production of apolypeptide &/or of another expressed biological molecule having auseful property.

Novel biological molecules whose manufacture is taught by this inventioninclude genes, gene pathways, and any molecules whose expression isaffected thereby, including directly encoded polypetides &/or anymolecules affected by such polypeptides. Said novel biological moleculesinclude those that contain a carbohydrate, a lipid, a nucleic acid, &/ora protein component, and specific but non-limiting examples of theseinclude antibiotics, antibodies, enzymes, and steroidal andnon-steroidal hormones.

In a particular non-limiting aspect, the present invention relates toenzymes, particularly to thermostable enzymes, and to their generationby directed evolution. More particularly, the present invention relatesto thermostable enzymes which are stable at high temperatures and whichhave improved activity at lower temperatures.

BACKGROUND OF THE INVENTION General Overview of the Problem to Be SolvedBrief Summary

It is instantly appreciated that harvesting the full potential ofnature's diversity can include both the step of discovery and the stepof optimizing what is discovered. For example, the step of discoveryallows one to mine biological molecules that have commercial utility. Itis instantly appreciated that the ability to harvest the full richnessof biodiversity, i.e. to mine biological molecules from a wide range ofenvironmental conditions, is critical to the ability to discover novelmolecules adapted to function under a wide variety of conditions,including extremes of conditions, such as may be found in a commercialapplication.

However, it is also instantly appreciated that only occasionally arethere criteria for selection &/or survival in nature that point in theexact direction of particular commercial needs. Instead, it is often thecase that a naturally occurring molecule will require a certain amountof change—from fine tuning to sweeping modification—in order to fulfilla particular unmet commercial need. Thus, to meet certain commercialneeds (e.g., a need for a molecule that is functional under a specificset of commercial processing conditions) it is sometimes advantageous toexperimentally modify a naturally expressed molecule to achieveproperties beyond what natural evolution has provided &/or is likely toprovide in the near future.

The approach, termed directed evolution, of experimentally modifying abiological molecule towards a desirable property, can be achieved bymutagenizing one or more parental molecular templates and by identifyingany desirable molecules among the progeny molecules. Currently availabletechnologies in directed evolution include methods for achievingstochastic (i.e. random) mutagenesis and methods for achievingnon-stochastic (non-random) mutagenesis. However, critical shortfalls inboth types of methods are identified in the instant disclosure.

In prelude, it is noteworthy that it may be argued philosophically bysome that all mutagenesis—if considered from an objective point ofview—is non-stochastic; and furthermore that the entire universe isundergoing a process that—if considered from an objective point ofview—is non-stochastic. Whether this is true is outside of the scope ofthe instant consideration. Accordingly, as used herein, the terms“randomness”, “uncertainty”, and “unpredictability” have subjectivemeanings, and the knowledge, particularly the predictive knowledge, ofthe designer of an experimental process is a determinant of whether theprocess is stochastic or non-stochastic.

By way of illustration, stochastic or random mutagenesis is exemplifiedby a situation in which a progenitor molecular template is mutated(modified or changed) to yield a set of progeny molecules havingmutation(s) that are not predetermined. Thus, in an in vitro stochasticmutagenesis reaction, for example, there is not a particularpredetermined product whose production is intended; rather there is anuncertainty—hence randomness—regarding the exact nature of the mutationsachieved, and thus also regarding the products generated. In contrast,non-stochastic or non-random mutagenesis is exemplified by a situationin which a progenitor molecular template is mutated (modified orchanged) to yield a progeny molecule having one or more predeterminedmutations. It is appreciated that the presence of background products insome quantity is a reality in many reactions where molecular processingoccurs, and the presence of these background products does not detractfrom the non-stochastic nature of a mutagenesis process having apredetermined product.

Thus, as used herein, stochastic mutagenesis is manifested in processessuch as error-prone PCR and stochastic shuffling, where the mutation(s)achieved are random or not predetermined. In contrast, as used herein,non-stochastic mutagenesis is manifested in instantly disclosedprocesses such as gene site-saturation mutagenesis and syntheticligation reassembly, where the exact chemical structure(s) of theintended product(s) are predetermined.

In brief, existing mutagenesis methods that are non-stochastic have beenserviceable in generating from one to only a very small number ofpredetermined mutations per method application, and thus produce permethod application from one to only a few progeny molecules that havepredetermined molecular structures. Moreover, the types of mutationscurrently available by the application of these non-stochastic methodsare also limited, and thus so are the types of progeny mutant molecules.

In contrast, existing methods for mutagenesis that are stochastic innature have been serviceable for generating somewhat larger numbers ofmutations per method application—though in a random fashion & usuallywith a large but unavoidable contingency of undesirable backgroundproducts. Thus, these existing stochastic methods can produce per methodapplication larger numbers of progeny molecules, but that haveundetermined molecular structures. The types of mutations that can beachieved by application of these current stochastic methods are alsolimited, and thus so are the types of progeny mutant molecules.

It is instantly appreciated that there is a need for the development ofnon-stochastic mutagenesis methods that:

1) Can be used to generate large numbers of progeny molecules that havepredetermined molecular structures;

2) Can be used to readily generate more types of mutations;

3) Can produce a correspondingly larger variety of progeny mutantmolecules;

4) Produce decreased unwanted background products;

5) Can be used in a manner that is exhaustive of all possibilities; and

6) Can produce progeny molecules in a systematic & non-repetitive way.

The instant invention satisfies all of these needs.

Directed Evolution Supplements Natural Evolution

Natural evolution has been a springboard for directed or experimentalevolution, serving both as a reservoir of methods to be mimicked and ofmolecular templates to be mutagenized. It is appreciated that, despiteits intrinsic process-related limitations (in the types of favored &/orallowed mutagenesis processes) and in its speed, natural evolution hashad the advantage of having been in process for millions of years & andthroughout a wide diversity of environments. Accordingly, naturalevolution (molecular mutagenesis and selection in nature) has resultedin the generation of a wealth of biological compounds that have shownusefulness in certain commercial applications.

However, it is instantly appreciated that many unmet commercial needsare discordant with any evolutionary pressure &/or direction that can befound in nature. Moreover, it is often the case that when commerciallyuseful mutations would otherwise be favored at the molecular level innature, natural evolution often overrides the positive selection of suchmutations, e.g. when there is a concurrent detriment to an organism as awhole (such as when a favorable mutation is accompanied by a detrimentalmutation). Additionally, natural evolution is often slow, and favorsfidelity in many types of replication. Additionally still, naturalevolution often favors a path paved mainly by consecutive beneficialmutations while tending to avoid a plurality of successive negativemutations, even though such negative mutations may prove beneficial whencombined, or may lead—through a circuitous route—to final state that isbeneficial.

Moreover, natural evolution advances through specific steps (e.g.specific mutagenesis and selection processes), with avoidance of lessfavored steps. For example, many nucleic acids do not reach close enoughproximity to each other in a operative environment to undergochimerization or incorporation or other types of transfers from onespecies to another. Thus, e.g., when sexual intercourse between 2particular species is avoided in nature, the chimerization of nucleicacids from these 2 species is likewise unlikely, with parasites commonto the two species serving as an example of a very slow passageway forinter-molecular encounters and exchanges of DNA. For another example,the generation of a molecule causing self-toxicity or self-lethality orsexual sterility is avoided in nature. For yet another example, thepropagation of a molecule having no particular immediate benefit to anorganism is prone to vanish in subsequent generations of the organism.Furthermore, e.g., there is no selection pressure for improving theperformance of molecule under conditions other than those to which it isexposed in its endogenous environment; e.g. a cytoplasmic molecule isnot likely to acquire functional features extending beyond what isrequired of it in the cytoplasm. Furthermore still, the propagation of abiological molecule is susceptible to any global detrimentaleffects—whether caused by itself or not—on its ecosystem. These andother characteristics greatly limit the types of mutations that can bepropagated in nature.

On the other hand, directed (or experimental) evolution—particularly asprovided herein—can be performed much more rapidly and can be directedin a more streamlined manner at evolving a predetermined molecularproperty that is commercially desirable where nature does not provideone &/or is not likely to provide. Moreover, the directed evolutioninvention provided herein can provide more wide-ranging possibilities inthe types of steps that can be used in mutagenesis and selectionprocesses. Accordingly, using templates harvested from nature, theinstant directed evolution invention provides more wide-rangingpossibilities in the types of progeny molecules that can be generatedand in the speed at which they can be generated than often nature itselfmight be expected to in the same length of time.

In a particular exemplification, the instantly disclosed directedevolution methods can be applied iteratively to produce a lineage ofprogeny molecules (e.g. comprising successive sets of progeny molecules)that would not likely be propagated (i.e., generated &/or selected for)in nature, but that could lead to the generation of a desirabledownstream mutagenesis product that is not achievable by naturalevolution.

Previous Directed Evolution Methods Are Suboptimal

Mutagenesis has been attempted in the past on many occasions, but bymethods that are inadequate for the purpose of this invention. Forexample, previously described non-stochastic methods have beenserviceable in the generation of only very small sets of progenymolecules (comprised often of merely a solitary progeny molecule). Byway of illustration, a chimeric gene has been made by joining 2polynucleotide fragments using compatible sticky ends generated byrestriction enzyme(s), where each fragment is derived from a separateprogenitor (or parental) molecule. Another example might be themutagenesis of a single codon position (i.e. to achieve a codonsubstitution, addition, or deletion) in a parental polynucleotide togenerate a single progeny polynucleotide encoding for a singlesite-mutagenized polypeptide.

Previous non-stochastic approaches have only been serviceable in thegeneration of but one to a few mutations per method application. Thus,these previously described non-stochastic methods thus fail to addressone of the central goals of this invention, namely the exhaustive andnon-stochastic chimerization of nucleic acids. Accordingly previousnon-stochastic methods leave untapped the vast majority of the possiblepoint mutations, chimerizations, and combinations thereof, which maylead to the generation of highly desirable progeny molecules.

In contrast, stochastic methods have been used to achieve larger numbersof point mutations and/or chimerizations than non-stochastic methods;for this reason, stochastic methods have comprised the predominantapproach for generating a set of progeny molecules that can be subjectedto screening, and amongst which a desirable molecular species mighthopefully be found. However, a major drawback of these approaches isthat—because of their stochastic nature—there is a randomness to theexact components in each set of progeny molecules that is produced.Accordingly, the experimentalist typically has little or no idea whatexact progeny molecular species are represented in a particular reactionvessel prior to their generation. Thus, when a stochastic procedure isrepeated (e.g. in a continuation of a search for a desirable progenymolecule), the re-generation and re-screening of previously discardedundesirable molecular species becomes a labor-intensive obstruction toprogress, causing a circuitous—if not circular—path to be taken. Thedrawbacks of such a highly suboptimal path can be addressed bysubjecting a stochastically generated set of progeny molecules to alabor-incurring process, such as sequencing, in order to identify theirmolecular structures, but even this is an incomplete remedy.

Moreover, current stochastic approaches are highly unsuitable forcomprehensively or exhaustively generating all the molecular specieswithin a particular grouping of mutations, for attributing functionalityto specific structural groups in a template molecule (e.g. a specificsingle amino acid position or a sequence comprised of two or more aminoacids positions), and for categorizing and comparing specific groupingof mutations. Accordingly, current stochastic approaches do notinherently enable the systematic elimination of unwanted mutagenesisresults, and are, in sum, burdened by too many inherently shortcomingsto be optimal for directed evolution.

In a non-limiting aspect, the instant invention addresses these problemsby providing non-stochastic means for comprehensively and exhaustivelygenerating all possible point mutations in a parental template. Inanother non-limiting aspect, the instant invention further providesmeans for exhaustively generating all possible chimerizations within agroup of chimerizations. Thus, the aforementioned problems are solved bythe instant invention.

Specific shortfalls in the technological landscape addressed by thisinvention include:

1) Site-directed mutagenesis technologies, such as sloppy orlow-fidelity PCR, are ineffective for systematically achieving at eachposition (site) along a polypeptide sequence the full (saturated) rangeof possible mutations (i.e. all possible amino acid substitutions).

2) There is no relatively easy systematic means for rapidly analyzingthe large amount of information that can be contained in a molecularsequence and in the potentially colossal number or progeny moleculesthat could be conceivably obtained by the directed evolution of one ormore molecular templates.

3) There is no relatively easy systematic means for providingcomprehensive empirical information relating structure to function formolecular positions.

4) There is no easy systematic means for incorporating internalcontrols, such as positive controls, for key steps in certainmutagenesis (e.g. chimerization) procedures.

5) There is no easy systematic means to select for a specific group ofprogeny molecules, such as full-length chimeras, from among smallerpartial sequences.

An exceedingly large number of possibilities exist for the purposefuland random combination of amino acids within a protein to produce usefulhybrid proteins and their corresponding biological molecules encodingfor these hybrid proteins, i.e., DNA, RNA. Accordingly, there is a needto produce and screen a wide variety of such hybrid proteins for adesirable utility, particularly widely varying random proteins.

The complexity of an active sequence of a biological macromolecule(e.g., polynucleotides, polypeptides, and molecules that are comprisedof both polynucleotide and polypeptide sequences) has been called itsinformation content (“IC”), which has been defined as the resistance ofthe active protein to amino acid sequence variation (calculated from theminimum number of invariable amino acids (bits) required to describe afamily of related sequences with the same function). Proteins that aremore sensitive to random mutagenesis have a high information content.

Molecular biology developments, such as molecular libraries, haveallowed the identification of quite a large number of variable bases,and even provide ways to select functional sequences from randomlibraries. In such libraries, most residues can be varied (althoughtypically not all at the same time) depending on compensating changes inthe context. Thus, while a 100 amino acid protein can contain only 2,000different mutations, 20¹⁰⁰ sequence combinations are possible.

Information density is the IC per unit length of a sequence. Activesites of enzymes tend to have a high information density. By contrast,flexible linkers of information in enzymes have a low informationdensity.

Current methods in widespread use for creating alternative proteins in alibrary format are error-prone polymerase chain reactions and cassettemutagenesis, in which the specific region to be optimized is replacedwith a synthetically mutagenized oligonucleotide. In both cases, asubstantial number of mutant sites are generated around certain sites inthe original sequence.

Error-prone PCR uses low-fidelity polymerization conditions to introducea low level of point mutations randomly over a long sequence. In amixture of fragments of unknown sequence, error-prone PCR can be used tomutagenize the mixture. The published error-prone PCR protocols sufferfrom a low processivity of the polymerase. Therefore, the protocol isunable to result in the random mutagenesis of an average-sized gene.This inability limits the practical application of error-prone PCR. Somecomputer simulations have suggested that point mutagenesis alone mayoften be too gradual to allow the large-scale block changes that arerequired for continued and dramatic sequence evolution. Further, thepublished error-prone PCR protocols do not allow for amplification ofDNA fragments greater than 0.5 to 1.0 kb, limiting their practicalapplication. In addition, repeated cycles of error-prone PCR can lead toan accumulation of neutral mutations with undesired results, such asaffecting a protein's immunogenicity but not its binding affinity.

In oligonucleotide-directed mutagenesis, a short sequence is replacedwith a synthetically mutagenized oligonucleotide. This approach does notgenerate combinations of distant mutations and is thus notcombinatorial. The limited library size relative to the vast sequencelength means that many rounds of selection are unavoidable for proteinoptimization. Mutagenesis with synthetic oligonucleotides requiressequencing of individual clones after each selection round followed bygrouping them into families, arbitrarily choosing a single family, andreducing it to a consensus motif. Such motif is re-synthesized andreinserted into a single gene followed by additional selection. Thisstep process constitutes a statistical bottleneck, is labor intensive,and is not practical for many rounds of mutagenesis.

Error-prone PCR and oligonucleotide-directed mutagenesis are thus usefulfor single cycles of sequence fine tuning, but rapidly become toolimiting when they are applied for multiple cycles.

Another limitation of error-prone PCR is that the rate of down-mutationsgrows with the information content of the sequence. As the informationcontent, library size, and mutagenesis rate increase, the balance ofdown-mutations to up-mutations will statistically prevent the selectionof further improvements (statistical ceiling).

In cassette mutagenesis, a sequence block of a single template istypically replaced by a (partially) randomized sequence. Therefore, themaximum information content that can be obtained is statisticallylimited by the number of random sequences (i.e., library size). Thiseliminates other sequence families which are not currently best, butwhich may have greater long term potential.

Also, mutagenesis with synthetic oligonucleotides requires sequencing ofindividual clones after each selection round. Thus, such an approach istedious and impractical for many rounds of mutagenesis.

Thus, error-prone PCR and cassette mutagenesis are best suited, and havebeen widely used, for fine-tuning areas of comparatively low informationcontent. One apparent exception is the selection of an RNA ligaseribozyme from a random library using many rounds of amplification byerror-prone PCR and selection.

In nature, the evolution of most organisms occurs by natural selectionand sexual reproduction. Sexual reproduction ensures mixing andcombining of the genes in the offspring of the selected individuals.During meiosis, homologous chromosomes from the parents line up with oneanother and cross-over part way along their length, thus randomlyswapping genetic material. Such swapping or shuffling of the DNA allowsorganisms to evolve more rapidly.

In recombination, because the inserted sequences were of proven utilityin a homologous environment, the inserted sequences are likely to stillhave substantial information content once they are inserted into the newsequence.

Theoretically there are 2,000 different single mutants of a 100 aminoacid protein. However, a protein of 100 amino acids has 20¹⁰⁰ possiblesequence combinations, a number which is too large to exhaustivelyexplore by conventional methods. It would be advantageous to develop asystem which would allow generation and screening of all of thesepossible combination mutations.

Some workers in the art have utilized an in vivo site specificrecombination system to generate hybrids of combine light chain antibodygenes with heavy chain antibody genes for expression in a phage system.However, their system relies on specific sites of recombination and islimited accordingly. Simultaneous mutagenesis of antibody CDR regions insingle chain antibodies (scFv) by overlapping extension and PCR havebeen reported.

Others have described a method for generating a large population ofmultiple hybrids using random in vivo recombination. This methodrequires the recombination of two different libraries of plasmids, eachlibrary having a different selectable marker. The method is limited to afinite number of recombinations equal to the number of selectablemarkers existing, and produces a concomitant linear increase in thenumber of marker genes linked to the selected sequence(s).

In vivo recombination between two homologous, but truncated,insect-toxin genes on a plasmid has been reported as a method ofproducing a hybrid gene. The in vivo recombination of substantiallymismatched DNA sequences in a host cell having defective mismatch repairenzymes, resulting in hybrid molecule formation has been reported.

SUMMARY OF THE INVENTION

This invention relates generally to the field of nucleic acidengineering and correspondingly encoded recombinant protein engineering.More particularly, the invention relates to the directed evolution ofnucleic acids and screening of clones containing the evolved nucleicacids for resultant activity(ies) of interest, such nucleic acidactivity(ies) &/or specified protein, particularly enzyme, activity(ies)of interest.

Mutagenized molecules provided by this invention may have chimericmolecules and molecules with point mutations, including biologicalmolecules that contain a carbohydrate, a lipid, a nucleic acid, &/or aprotein component, and specific but non-limiting examples of theseinclude antibiotics, antibodies, enzymes, and steroidal andnon-steroidal hormones.

This invention relates generally to a method of: 1) preparing a progenygeneration of molecule(s) (including a molecule that is comprised of apolynucleotide sequence, a molecule that is comprised of a polypeptidesequence, and a molecules that is comprised in part of a polynucleotidesequence and in part of a polypeptide sequence), that is mutagenized toachieve at least one point mutation, addition, deletion, &/orchimerization, from one or more ancestral or parental generationtemplate(s); 2) screening the progeny generation molecule(s)—preferablyusing a high throughput method—for at least one property of interest(such as an improvement in an enzyme activity or an increase instability or a novel chemotherapeutic effect); 3) optionally obtaining&/or cataloguing structural &/or and functional information regardingthe parental &/or progeny generation molecules; and 4) optionallyrepeating any of steps 1) to 3).

In a preferred embodiment, there is generated (e.g. from a parentpolynucleotide template)—in what is termed “codon site-saturationmutagenesis”—a progeny generation of polynucleotides, each having atleast one set of up to three contiguous point mutations (i.e. differentbases comprising a new codon), such that every codon (or every family ofdegenerate codons encoding the same amino acid) is represented at eachcodon position. Corresponding to—and encoded by—this progeny generationof polynucleotides, there is also generated a set of progenypolypeptides, each having at least one single amino acid point mutation.In a preferred aspect, there is generated—in what is termed “amino acidsite-saturation mutagenesis”—one such mutant polypeptide for each of the19 naturally encoded polypeptide-forming alpha-amino acid substitutionsat each and every amino acid position along the polypeptide. Thisyields—for each and every amino acid position along the parentalpolypeptide—a total of 20 distinct progeny polypeptides including theoriginal amino acid, or potentially more than 21 distinct progenypolypeptides if additional amino acids are used either instead of or inaddition to the 20 naturally encoded amino acids

Thus, in another aspect, this approach is also serviceable forgenerating mutants containing—in addition to &/or in combination withthe 20 naturally encoded polypeptide-forming alpha-amino acids—otherrare &/or not naturally-encoded amino acids and amino acid derivatives.In yet another aspect, this approach is also serviceable for generatingmutants by the use of—in addition to &/or in combination with natural orunaltered codon recognition systems of suitable hosts—altered,mutagenized, &/or designer codon recognition systems (such as in a hostcell with one or more altered tRNA molecules).

In yet another aspect, this invention relates to recombination and morespecifically to a method for preparing polynucleotides encoding apolypeptide by a method of in vivo reassortment of polynucleotidesequences containing regions of partial homology, assembling thepolynucleotides to form at least one polynucleotide and screening thepolynucleotides for the production of polypeptide(s) having a usefulproperty.

In yet another preferred embodiment, this invention is serviceable foranalyzing and cataloguing—with respect to any molecular property (e.g.an enzymatic activity) or combination of properties allowed by currenttechnology—the effects of any mutational change achieved (includingparticularly saturation mutagenesis). Thus, a comprehensive method isprovided for determining the effect of changing each amino acid in aparental polypeptide into each of at least 19 possible substitutions.This allows each amino acid in a parental polypeptide to becharacterized and catalogued according to its spectrum of potentialeffects on a measurable property of the polypeptide.

In another aspect, the method of the present invention utilizes thenatural property of cells to recombine molecules and/or to mediatereductive processes that reduce the complexity of sequences and extentof repeated or consecutive sequences possessing regions of homology.

It is an object of the present invention to provide a method forgenerating hybrid polynucleotides encoding biologically active hybridpolypeptides with enhanced activities. In accomplishing these and otherobjects, there has been provided, in accordance with one aspect of theinvention, a method for introducing polynucleotides into a suitable hostcell and growing the host cell under conditions that produce a hybridpolynucleotide.

In another aspect of the invention, the invention provides a method forscreening for biologically active hybrid polypeptides encoded by hybridpolynucleotides. The present method allows for the identification ofbiologically active hybrid polypeptides with enhanced biologicalactivities.

According to another aspect of this invention is provided that animportant advantage of the synthetic ligation reassembly methodsprovided herein is that the starting templates that can be aligned andsubjected to ligation reassembly are not limited to full length genes.In fact when working with genomic sequences it is often the case thatpartial gene sequences are obtained, and these can be subjected toligation reassembly according to this invention.

In an important aspect of this invention, it is appreciated herein thatnucleic acid building blocks that are serviceable for this invention canbe generated by synthetic means or alternatively by polymerase-basedmethods either in vivo or in vitro or alternatively by a combination ofsynthetic means and polymerase-based means. The likelihood of nucleotideincorporation errors is different for each method. Among such errorssome may be undesirable at times. For example the presence of a singlenucleotide mistake in the generation of up a nucleic acid building blockcan lead to the undesirable introduction of a stop codon. It isappreciated that several prescreening methods can be used to filter outto undesirable nucleotide incorporation errors. For example thefinalized construct can be a fusion product that includes a reportersequence, such as GFP or a 6×His tag, that is only generated in theabsence of unwanted internal stop codons. It is also appreciated thatthe selection all of the method by which nucleic acid building blocksare generated can be based upon consideration of the error rates of eachmethod considered.

Furthermore, it is provided that, according to this invention, nucleicacid building blocks may be single-stranded or double-strandedpolynucleotides. Thus, ligation reassembly according to this inventionmay be performed using synthetic as well as non-synthetic nucleic acidbuilding blocks up, or a combination thereof. Moreover bothsingle-stranded and double-stranded polynucleotides may be used inligation reassembly, either mutually exclusively or in combination.

In another aspect of this invention of, it is provided that blunt endedacid building blocks may be used without alteration of the blunt ends oralternatively may be subjected to treatment with an exonuclease, such asExonuclease III, to create serviceable overhangs up for syntheticligation couplings of. Such a treatment may be brief and controlled,e.g., by subjecting the working sample of to a temperature at which theExonuclease III is operable, and then quickly chilling. In all aspectsof ligation reassembly, treatment with a ligase such as T4 DNA Ligase isan optional step.

In specific embodiments, the invention provides a method ofnon-stochastically producing a library of chimeric nucleic acidmolecules having an overall assembly order that is chosen by design,which method is comprised of (a) generating by design a plurality ofspecific synthetic nucleic acid building blocks having serviceablemutually compatible ligatable ends, and (b) assembling these nucleicacid building blocks, such that a designed overall assembly order isachieved; whereby a set of progenitor templates, such as genes (e.g. afamily of esterase genes) or genes pathways (e.g. encoding antibiotics)can be shuffled to generate a sizable library of progeny polynucleotidemolecules (e.g. 10¹⁰⁰) and correspondingly encoded polypeptides, andwhereby the expression screening of the progeny polynucleotide libraryprovides a means to identify a desirable species that has a desirableproperty, such as a specific enzymatic activity serviceable for acommercial application.

Also included is a method of non-stochastically producing a librarycomprised of a defined number of groupings comprised of one or moregroupings of chimeric nucleic acid molecules having an overall assemblyorder that is chosen by design, which method is comprised of (a)generating by design for each grouping a set of specific nucleic acidbuilding blocks having serviceable mutually compatible ligatable ends,and (b) assembling these nucleic acid building blocks according to saidgroupings, such that a designed overall assembly order is achieved;whereby a set of progenitor templates, such as genes (e.g. a family ofesterase genes) or genes pathways (e.g. encoding antibiotics) can beshuffled to generate a sizable library of progeny polynucleotidemolecules (e.g. 10¹⁰⁰) and correspondingly encoded polypeptides, andwhereby the expression screening of the progeny polynucleotide libraryprovides a means to identify a desirable species that has a desirableproperty, such as a specific enzymatic activity serviceable for acommercial application.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating preferred embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Exonuclease Activity. FIG. 1 shows the activity of the enzymeexonuclease III. This is an exemplary enzyme that can be used toshuffle, assemble, reassemble, recombine, and/or concatenatepolynucleotide building blocks. The asterisk indicates that the enzymeacts from the 3′ direction towards the 5′ direction of thepolynucleotide substrate.

FIG. 2. Generation of A Nucleic Acid Building Block by Polymerase-BasedAmplification. FIG. 2 illustrates a method of generating adouble-stranded nucleic acid building block with two overhangs using apolymerase-based amplification reaction (e.g., PCR). As illustrated, afirst polymerase-based amplification reaction using a first set ofprimers, F₂ and R₁, is used to generate a blunt-ended product (labeledReaction 1, Product 1), which is essentially identical to Product A. Asecond polymerase-based amplification reaction using a second set ofprimers, F₁ and R₂, is used to generate a blunt-ended product (labeledReaction 2, Product 2), which is essentially identical to Product B.These two products are then mixed and allowed to melt and anneal,generating a potentially useful double-stranded nucleic acid buildingblock with two overhangs. In the example of FIG. 1, the product with the3′ overhangs (Product C) is selected for by nuclease-based degradationof the other 3 products using a 3′ acting exonuclease, such asexonuclease III. Alternate primers are shown in parenthesis toillustrate serviceable primers may overlap, and additionally thatserviceable primers may be of different lengths, as shown.

FIG. 3. Unique Overhangs And Unique Couplings. FIG. 3 illustrates thepoint that the number of unique overhangs of each size (e.g. the totalnumber of unique overhangs composed of 1 or 2 or 3, etc. nucleotides)exceeds the number of unique couplings that can result from the use ofall the unique overhangs of that size. For example, there are 4 unique3′ overhangs composed of a single nucleotide, and 4 unique 5′ overhangscomposed of a single nucleotide. Yet the total number of uniquecouplings that can be made using all the 8 unique single-nucleotide 3′overhangs and single-nucleotide 5′ overhangs is 4.

FIG. 4. Unique Overall Assembly Order Achieved by Sequentially Couplingthe Building BlocksFigure 4 illustrates the fact that in order toassemble a total of “n” nucleic acid building blocks, “n−1” couplingsare needed. Yet it is sometimes the case that the number of uniquecouplings available for use is fewer that the “n−1” value. Under these,and other, circumstances a stringent non-stochastic overall assemblyorder can still be achieved by performing the assembly process insequential steps. In this example, 2 sequential steps are used toachieve a designed overall assembly order for five nucleic acid buildingblocks. In this illustration the designed overall assembly order for thefive nucleic acid building blocks is: 5′-(#1-#2-#3-#4-#5)-3′, where #1represents building block number 1, etc.

FIG. 5. Unique Couplings Available Using a Two-Nucleotide 3′ Overhang.FIG. 5 further illustrates the point that the number of unique overhangsof each size (here, e.g. the total number of unique overhangs composedof 2 nucleotides) exceeds the number of unique couplings that can resultfrom the use of all the unique overhangs of that size. For example,there are 16 unique 3′ overhangs composed of two nucleotides, andanother 16 unique 5′ overhangs composed of two nucleotides, for a totalof 32 as shown. Yet the total number of couplings that are unique andnot self-binding that can be made using all the 32 uniquedouble-nucleotide 3′ overhangs and double-nucleotide 5′ overhangs is 12.Some apparently unique couplings have “identical twins” (marked in thesame shading), which are visually obvious in this illustration. Stillother overhangs contain nucleotide sequences that can self-bind in apalindromic fashion, as shown and labeled in this figure; thus they notcontribute the high stringency to the overall assembly order.

FIG. 6. Generation of an Exhaustive Set of Chimeric Combinations bySynthetic Ligation Reassembly. FIG. 6 showcases the power of thisinvention in its ability to generate exhaustively and systematically allpossible combinations of the nucleic acid building blocks designed inthis example. Particularly large sets (or libraries) of progeny chimericmolecules can be generated. Because this method can be performedexhaustively and systematically, the method application can be repeatedby choosing new demarcation points and with correspondingly newlydesigned nucleic acid building blocks, bypassing the burden ofre-generating and re-screening previously examined and rejectedmolecular species. It is appreciated that, codon wobble can be used toadvantage to increase the frequency of a demarcation point. In otherwords, a particular base can often be substituted into a nucleic acidbuilding block without altering the amino acid encoded by progenitorcodon (that is now altered codon) because of codon degeneracy. Asillustrated, demarcation points are chosen upon alignment of 8progenitor templates. Nucleic acid building blocks including theiroverhangs (which are serviceable for the formation of ordered couplings)are then designed and synthesized. In this instance, 18 nucleic acidbuilding blocks are generated based on the sequence of each of the 8progenitor templates, for a total of 144 nucleic acid building blocks(or double-stranded oligos). Performing the ligation synthesis procedurewill then produce a library of progeny molecules comprised of yield of8¹⁸ (or over 1.8×10¹⁶) chimeras.

FIG. 7. Synthetic genes from oligos. According to one embodiment of thisinvention, double-stranded nucleic acid building blocks are designed byaligning a plurality of progenitor nucleic acid templates. Preferablythese templates contain some homology and some heterology. The nucleicacids may encode related proteins, such as related enzymes, whichrelationship may be based on function or structure or both. FIG. 7 showsthe alignment of three polynucleotide progenitor templates and theselection of demarcation points (boxed) shared by all the progenitormolecules. In this particular example, the nucleic acid building blocksderived from each of the progenitor templates were chosen to beapproximately 30 to 50 nucleotides in length.

FIG. 8. Nucleic acid building blocks for synthetic ligation genereassembly. FIG. 8 shows the nucleic acid building blocks from theexample in FIG. 7. The nucleic acid building blocks are shown here ingeneric cartoon form, with their compatible overhangs, including both 5′and 3′ overhangs. There are 22 total nucleic acid building blocksderived from each of the 3 progenitor templates. Thus, the ligationsynthesis procedure can produce a library of progeny molecules comprisedof yield of 3²² (or over 3.1×10¹⁰) chimeras.

FIG. 9. Addition of Introns by Synthetic Ligation Reassembly. FIG. 9shows in generic cartoon form that an intron may be introduced into achimeric progeny molecule by way of a nucleic acid building block. It isappreciated that introns often have consensus sequences at both terminiin order to render them operational. It is also appreciated that, inaddition to enabling gene splicing, introns may serve an additionalpurpose by providing sites of homology to other nucleic acids to enablehomologous recombination. For this purpose, and potentially others, itmay be sometimes desirable to generate a large nucleic acid buildingblock for introducing an intron. If the size is overly large easilygenerating by direct chemical synthesis of two single stranded oligos,such a specialized nucleic acid building block may also be generated bydirect chemical synthesis of more than two single stranded oligos or byusing a polymerase-based amplification reaction as shown in FIG. 2.

FIG. 10. Ligation Reassembly Using Fewer Than All The Nucleotides Of AnOverhang. FIG. 10 shows that coupling can occur in a manner that doesnot make use of every nucleotide in a participating overhang. Thecoupling is particularly lively to survive (e.g. in a transformed host)if the coupling reinforced by treatment with a ligase enzyme to formwhat may be referred to as a “gap ligation” or a “gapped ligation”. Itis appreciated that, as shown, this type of coupling can contribute togeneration of unwanted background product(s), but it can also be usedadvantageously increase the diversity of the progeny library generatedby the designed ligation reassembly.

FIG. 11. Avoidance of unwanted self-ligation in palindromic couplings.As mentioned before and shown in FIG. 5, certain overhangs are able toundergo self-coupling to form a palindromic coupling. A coupling isstrengthened substantially if it is reinforced by treatment with aligase enzyme. Accordingly, it is appreciated that the lack of 5′phosphates on these overhangs, as shown, can be used advantageously toprevent this type of palindromic self-ligation. Accordingly, thisinvention provides that nucleic acid building blocks can be chemicallymade (or ordered) that lack a 5′ phosphate group (or alternatively theycan be remove—e.g. by treatment with a phosphatase enzyme such as a calfintestinal alkaline phosphatase (CIAP)—in order to prevent palindromicself-ligations in ligation reassembly processes.

FIG. 12. Pathway Engineering. It is a goal of this invention to provideways of making new gene pathways using ligation reassembly, optionallywith other directed evolution methods such as saturation mutagenesis.FIG. 12 illustrates a preferred approach that may be taken to achievethis goal. It is appreciated that naturally-occurring microbial genepathways are linked more often than naturally-occurring eukaryotic (e.g.plant) gene pathways, which are sometime only partially linked. In aparticular embodiment, this invention provides that regulatory genesequences (including promoters) can be introduced in the form of nucleicacid building blocks into progeny gene pathways generated by ligationreassembly processes. Thus, originally linked microbial gene pathways,as well as originally unlinked genes and gene pathways, can be thusconverted to acquire operability in plants and other eukaryotes.

FIG. 13. Avoidance of unwanted self-ligation in palindromic couplings.FIG. 13 illustrates that another goal of this invention, in addition tothe generation of novel gene pathways, is the subjection of genepathways—both naturally occurring and man-made—to mutagenesis andselection in order to achieve improved progeny molecules using theinstantly disclosed methods of directed evolution (including saturationmutagenesis and synthetic ligation reassembly). In a particularembodiment, as provided by the instant invention, both microbial andplant pathways can be improved by directed evolution, and as shown, thedirected evolution process can be performed both on genes prior tolinking them into pathways, and on gene pathways themselves.

FIG. 14. Conversion of Microbial Pathways to Eukaryotic Pathways. In aparticular embodiment, this invention provides that microbial pathwayscan be converted to pathways operable in plants and other eukaryoticspecies by the introduction of regulatory sequences that function inthose species. Preferred regulatory sequences include promoters,operators, and activator binding sites. As shown, a preferred method ofachieving the introduction of such serviceable regulatory sequences isin the form of nucleic acid building blocks, particularly through theuse of couplings in ligation reassembly processes. These couplings inFIG. 14 are marked with the letters A, B, C, D and F.

FIG. 15. Evolution of polypeptides by synthesizing (in vivo or in vitro)corresponding deduced polynucleotides and subjecting the deducedpolynucleotides to directed evolution and expression screeningsubsequently expressed polypeptides. This invention provides thatligation reassembly and site saturation mutagenesis are each serviceablefor introducing nucleotide substitutions as well as nucleotide deletionsand nucleotide additions and combinations thereof. Furthermore syntheticligation reassembly can be performed on a plurality of startingtemplates as well as on a single template to rearrange the order of thenucleotide cassettes in a non-stochastic predetermined manner.Additionally, when subjecting a plurality of starting templates toligation reassembly, it is not necessary that the same number of nucleicacid building blocks be generated from each template (e.g. toparticipate to in each coupling). Thus for example if three templatesare used, then a different number of nucleic acid building blocks may begenerated corresponding to each template.

FIG. 16: In Silico Triage. This figure illustrates the grouping ofpotential products and the ranking of the groupings according to“structure-function” predictions, which steps are aspects of what isreferred to herein as “triaging”, and specifically “in silico triage” ifperformed using the aid of a computer.

FIG. 17: Solid Phase Ligation Reassembly

FIG. 18. Polynucleotide reassembly. Shown is an example of directedevolution. n different strains of a virus are used in this illustration,but the technique is applicable to any single nucleic acid as well as toany nucleic acid for which different strains, species, or gene familieshave homologous nucleic acids that have one or more nucleotide changescompared to other homologous nucleic acids. The different variantnucleic acids are experimentally generated, preferablynon-stochastically, as described herein, and screened or selected toidentify those variants that exhibit the desired property. The directedevolution method(s) and screening can be repeated one or more times toobtain further improvement. Panel B shows that successive rounds ofdirected evolution can produce progressively enhanced properties, andthat the combination of individual beneficial mutations can lead to anenhance improvement compared to the improvement achieved by anindividual beneficial mutation.

FIGS. 19A-C. An alignment of two CMV-derived nucleotide sequences fromhuman and primate species. Shown here is an alignment of two CMV-derivednucleotide sequences of human and primate strains. This alignment isserviceable for performing non-stochastic polynucleotide reassembly.Nucleotide sequences shared by 2 sequences are in red lettering toillustrate preferred but non-limiting examples of reassembly points.

FIG. 20: An alignment of the IFN-gamma nucleotide sequences from human,cat, rodent species. Shown here is an alignment of the IFN-gammanucleotide sequences from human, cat, and rodent species. This alignmentis serviceable for performing non-stochastic polynucleotide reassembly.Nucleotide sequences shared by 2 sequences are in blue lettering &nucleotide sequences shared by 3 sequences are in red lettering toillustrate preferred but non-limiting examples of reassembly points.

DEFINITIONS OF TERMS

In order to facilitate understanding of the examples provided herein,certain frequently occurring methods and/or terms will be described.

The term “agent” is used herein to denote a chemical compound, a mixtureof chemical compounds, an array of spatially localized compounds (e.g.,a VLSIPS peptide array, polynucleotide array, and/or combinatorial smallmolecule array), biological macromolecule, a bacteriophage peptidedisplay library, a bacteriophage antibody (e.g., scFv) display library,a polysome peptide display library, or an extract made form biologicalmaterials such as bacteria, plants, fungi, or animal (particularmammalian) cells or tissues. Agents are evaluated for potential activityas anti-neoplastics, anti-inflammatories or apoptosis modulators byinclusion in screening assays described hereinbelow. Agents areevaluated for potential activity as specific protein interactioninhibitors (i.e., an agent which selectively inhibits a bindinginteraction between two predetermined polypeptides but which doe snotsubstantially interfere with cell viability) by inclusion in screeningassays described hereinbelow.

An “ambiguous base requirement” in a restriction site refers to anucleotide base requirement that is not specified to the fullest extent,i.e. that is not a specific base (such as, in a non-limitingexemplification, a specific base selected from A, C, G, and T), butrather may be any one of at least two or more bases. Commonly acceptedabbreviations that are used in the art as well as herein to representambiguity in bases include the following: R=G or A; Y=C or T; M=A or C;K=G or T; S=G or C; W=A or T; H=A or C or T; B=G or T or C; V=G or C orA; D=G or A or T; N=A or C or G or T.

The term “amino acid” as used herein refers to any organic compound thatcontains an amino group (—NH₂) and a carboxyl group (—COOH); preferablyeither as free groups or alternatively after condensation as part ofpeptide bonds. The “twenty naturally encoded polypeptide-formingalpha-amino acids” are understood in the art and refer to: alanine (alaor A), arginine (arg or R), asparagine (asn or N), aspartic acid (asp orD), cysteine (cys or C), gluatamic acid (glu or E), glutamine (gln orQ), glycine (gly or G), histidine (his or H), isoleucine (ile or I),leucine (leu or L), lysine (lys or K), methionine (met or M),phenylalanine (phe or F), proline (pro or P), serine (ser or S),threonine (thr or T), tryptophan (trp or W), tyrosine (tyr or Y), andvaline (val or V).

The term “amplification” means that the number of copies of apolynucleotide is increased.

The term “antibody”, as used herein, refers to intact immunoglobulinmolecules, as well as fragments of immunoglobulin molecules, such asFab, Fab′, (Fab′)₂, Fv, and SCA fragments, that are capable of bindingto an epitope of an antigen. These antibody fragments, which retain someability to selectively bind to an antigen (e.g., a polypeptide antigen)of the antibody from which they are derived, can be made using wellknown methods in the art (see, e.g., Harlow and Lane, supra), and aredescribed further, as follows.

-   (1) An Fab fragment consists of a monovalent antigen-binding    fragment of an antibody molecule, and can be produced by digestion    of a whole antibody molecule with the enzyme papain, to yield a    fragment consisting of an intact light chain and a portion of a    heavy chain.-   (2) An Fab′ fragment of an antibody molecule can be obtained by    treating a whole antibody molecule with pepsin, followed by    reduction, to yield a molecule consisting of an intact light chain    and a portion of a heavy chain. Two Fab′ fragments are obtained per    antibody molecule treated in this manner.-   (3) An (Fab′)₂ fragment of an antibody can be obtained by treating a    whole antibody molecule with the enzyme pepsin, without subsequent    reduction. A (Fab′)₂ fragment is a dimer of two Fab′ fragments, held    together by two disulfide bonds.-   (4) An Fv fragment is defined as a genetically engineered fragment    containing the variable region of a light chain and the variable    region of a heavy chain expressed as two chains.-   (5) An single chain antibody (“SCA”) is a genetically engineered    single chain molecule containing the variable region of a light    chain and the variable region of a heavy chain, linked by a    suitable, flexible polypeptide linker.

The term “Applied Molecular Evolution” (“AME”) means the application ofan evolutionary design algorithm to a specific, useful goal. While manydifferent library formats for AME have been reported forpolynucleotides, peptides and proteins (phage, lad and polysomes), noneof these formats have provided for recombination by random cross-oversto deliberately create a combinatorial library.

A molecule that has a “chimeric property” is a molecule that is: 1) inpart homologous and in part heterologous to a first reference molecule;while 2) at the same time being in part homologous and in partheterologous to a second reference molecule; without 3) precluding thepossibility of being at the same time in part homologous and in partheterologous to still one or more additional reference molecules. In anon-limiting embodiment, a chimeric molecule may be prepared byassembling a reassortment of partial molecular sequences. In anon-limiting aspect, a chimeric polynucleotide molecule may be preparedby synthesizing the chimeric polynucleotide using plurality of moleculartemplates, such that the resultant chimeric polynucleotide hasproperties of a plurality of templates.

The term “cognate” as used herein refers to a gene sequence that isevolutionarily and functionally related between species. For example,but not limitation, in the human genome the human CD4 gene is thecognate gene to the mouse 3d4 gene, since the sequences and structuresof these two genes indicate that they are highly homologous and bothgenes encode a protein which functions in signaling T cell activationthrough MHC class II-restricted antigen recognition.

A “comparison window,” as used herein, refers to a conceptual segment ofat least 20 contiguous nucleotide positions wherein a polynucleotidesequence may be compared to a reference sequence of at least 20contiguous nucleotides and wherein the portion of the polynucleotidesequence in the comparison window may comprise additions or deletions(i.e., gaps) of 20 percent or less as compared to the reference sequence(which does not comprise additions or deletions) for optimal alignmentof the two sequences. Optimal alignment of sequences for aligning acomparison window may be conducted by the local homology algorithm ofSmith (Smith and Waterman, Adv Appl Math, 1981; Smith and Waterman, JTeor Biol, 1981; Smith and Waterman, J Mol Biol, 1981; Smith et al, JMol Evol, 1981), by the homology alignment algorithm of Needleman(Needleman and Wuncsch, 1970), by the search of similarity method ofPearson (Pearson and Lipman, 1988), by computerized implementations ofthese algorithms (GAP, BESTFIT, FASTA, and TFASTA in the WisconsinGenetics Software Package Release 7.0, Genetics Computer Group, 575Science Dr., Madison, Wis.), or by inspection, and the best alignment(i.e., resulting in the highest percentage of homology over thecomparison window) generated by the various methods is selected.

As used herein, the term “complementarity-determining region” and “CDR”refer to the art-recognized term as exemplified by the Kabat and ChothiaCDR definitions also generally known as supervariable regions orhypervariable loops (Chothia and Lesk, 1987; Clothia et al, 1989; Kabatet al, 1987; and Tramontano et al, 1990). Variable region domainstypically comprise the amino-terminal approximately 105-115 amino acidsof a naturally-occurring immunoglobulin chain (e.g., amino acids 1-110),although variable domains somewhat shorter or longer are also suitablefor forming single-chain antibodies.

“Conservative amino acid substitutions” refer to the interchangeabilityof residues having similar side chains. For example, a group of aminoacids having aliphatic side chains is glycine, alanine, valine, leucine,and isoleucine; a group of amino acids having aliphatic-hydroxyl sidechains is serine and threonine; a group of amino acids havingamide-containing side chains is asparagine and glutamine; a group ofamino acids having aromatic side chains is phenylalanine, tyrosine, andtryptophan; a group of amino acids having basic side chains is lysine,arginine, and histidine; and a group of amino acids havingsulfur-containing side chains is cysteine and methionine. Preferredconservative amino acids substitution groups are:valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine,alanine-valine, and asparagine-glutamine.

The term “corresponds to” is used herein to mean that a polynucleotidesequence is homologous (i.e., is identical, not strictly evolutionarilyrelated) to all or a portion of a reference polynucleotide sequence, orthat a polypeptide sequence is identical to a reference polypeptidesequence. In contradistinction, the term “complementary to” is usedherein to mean that the complementary sequence is homologous to all or aportion of a reference polynucleotide sequence. For illustration, thenucleotide sequence “TATAC” corresponds to a reference “TATAC” and iscomplementary to a reference sequence “GTATA.”

The term “degrading effective” amount refers to the amount of enzymewhich is required to process at least 50% of the substrate, as comparedto substrate not contacted with the enzyme. Preferably, at least 80% ofthe substrate is degraded.

As used herein, the term “defined sequence framework” refers to a set ofdefined sequences that are selected on a non-random basis, generally onthe basis of experimental data or structural data; for example, adefined sequence framework may comprise a set of amino acid sequencesthat are predicted to form a β-sheet structure or may comprise a leucinezipper heptad repeat motif, a zinc-finger domain, among othervariations. A “defined sequence kernal” is a set of sequences whichencompass a limited scope of variability. Whereas (1) a completelyrandom 10-mer sequence of the 20 conventional amino acids can be any of(20)¹⁰ sequences, and (2) a pseudorandom 10-mer sequence of the 20conventional amino acids can be any of (20)¹⁰ sequences but will exhibita bias for certain residues at certain positions and/or overall, (3) adefined sequence kernal is a subset of sequences if each residueposition was allowed to be any of the allowable 20 conventional aminoacids (and/or allowable unconventional amino/imino acids). A definedsequence kernal generally comprises variant and invariant residuepositions and/or comprises variant residue positions which can comprisea residue selected from a defined subset of amino acid residues), andthe like, either segmentally or over the entire length of the individualselected library member sequence. Defined sequence kernels can refer toeither amino acid sequences or polynucleotide sequences. Of illustrationand not limitation, the sequences (NNK)₁₀ and (NNM)₁₀, wherein Nrepresents A, T, G, or C; K represents G or T; and M represents A or C,are defined sequence kernels.

“Digestion” of DNA refers to catalytic cleavage of the DNA with arestriction enzyme that acts only at certain sequences in the DNA. Thevarious restriction enzymes used herein are commercially available andtheir reaction conditions, cofactors and other requirements were used aswould be known to the ordinarily skilled artisan. For analyticalpurposes, typically 1 μg of plasmid or DNA fragment is used with about 2units of enzyme in about 20 μl of buffer solution. For the purpose ofisolating DNA fragments for plasmid construction, typically 5 to 50 μgof DNA are digested with 20 to 250 units of enzyme in a larger volume.Appropriate buffers and substrate amounts for particular restrictionenzymes are specified by the manufacturer. Incubation times of about 1hour at 37° C. are ordinarily used, but may vary in accordance with thesupplier's instructions. After digestion the reaction is electrophoreseddirectly on a gel to isolate the desired fragment.

“Directional ligation” refers to a ligation in which a 5′ end and a 3′end of a polynucleotide are different enough to specify a preferredligation orientation. For example, an otherwise untreated and undigestedPCR product that has two blunt ends will typically not have a preferredligation orientation when ligated into a cloning vector digested toproduce blunt ends in its multiple cloning site; thus, directionalligation will typically not be displayed under these circumstances. Incontrast, directional ligation will typically displayed when a digestedPCR product having a 5′ EcoR I-treated end and a 3′ BamH I-is ligatedinto a cloning vector that has a multiple cloning site digested withEcoR I and BamH I.

The term “DNA shuffling” is used herein to indicate recombinationbetween substantially homologous but non-identical sequences, in someembodiments DNA shuffling may involve crossover via non-homologousrecombination, such as via cer/lox and/or flp/frt systems and the like.

As used in this invention, the term “epitope” refers to an antigenicdeterminant on an antigen, such as a phytase polypeptide, to which theparatope of an antibody, such as an phytase-specific antibody, binds.Antigenic determinants usually consist of chemically active surfacegroupings of molecules, such as amino acids or sugar side chains, andcan have specific three-dimensional structural characteristics, as wellas specific charge characteristics. As used herein “epitope” refers tothat portion of an antigen or other macromolecule capable of forming abinding interaction that interacts with the variable region binding bodyof an antibody. Typically, such binding interaction is manifested as anintermolecular contact with one or more amino acid residues of a CDR.

The terms “fragment”, “derivative” and “analog” when referring to areference polypeptide comprise a polypeptide which retains at least onebiological function or activity that is at least essentially same asthat of the reference polypeptide. Furthermore, the terms “fragment”,“derivative” or “analog” are exemplified by a “pro-form” molecule, suchas a low activity proprotein that can be modified by cleavage to producea mature enzyme with significantly higher activity.

A method is provided herein for producing from a template polypeptide aset of progeny polypeptides in which a “full range of single amino acidsubstitutions” is represented at each amino acid position. As usedherein, “full range of single amino acid substitutions” is in referenceto the naturally encoded 20 naturally encoded polypeptide-formingalpha-amino acids, as described herein.

The term “gene” means the segment of DNA involved in producing apolypeptide chain; it includes regions preceding and following thecoding region (leader and trailer) as well as intervening sequences(introns) between individual coding segments (exons).

“Genetic instability”, as used herein, refers to the natural tendency ofhighly repetitive sequences to be lost through a process of reductiveevents generally involving sequence simplification through the loss ofrepeated sequences. Deletions tend to involve the loss of one copy of arepeat and everything between the repeats.

The term “heterologous” means that one single-stranded nucleic acidsequence is unable to hybridize to another single-stranded nucleic acidsequence or its complement. Thus areas of heterology means that areas ofpolynucleotides or polynucleotides have areas or regions within theirsequence which are unable to hybridize to another nucleic acid orpolynucleotide. Such regions or areas are for example areas ofmutations.

The term “homologous” or “homeologous” means that one single-strandednucleic acid nucleic acid sequence may hybridize to a complementarysingle-stranded nucleic acid sequence. The degree of hybridization maydepend on a number of factors including the amount of identity betweenthe sequences and the hybridization conditions such as temperature andsalt concentrations as discussed later. Preferably the region ofidentity is greater than about 5 bp, more preferably the region ofidentity is greater than 10 bp.

An immunoglobulin light or heavy chain variable region consists of a“framework” region interrupted by three hypervariable regions, alsocalled CDR's. The extent of the framework region and CDR's have beenprecisely defined; see “Sequences of Proteins of Immunological Interest”(Kabat et al, 1987). The sequences of the framework regions of differentlight or heavy chains are relatively conserved within a specie. As usedherein, a “human framework region” is a framework region that issubstantially identical (about 85 or more, usually 90-95 or more) to theframework region of a naturally occurring human immunoglobulin. theframework region of an antibody, that is the combined framework regionsof the constituent light and heavy chains, serves to position and alignthe CDR's. The CDR's are primarily responsible for binding to an epitopeof an antigen.

The benefits of this invention extend to “commercial applications” (orcommercial processes), which term is used to include applications incommercial industry proper (or simply industry) as well asnon-commercial commercial applications (e.g. biomedical research at anon-profit institution). Relevant applications include those in areas ofdiagnosis, medicine, agriculture, manufacturing, and academia.

The term “identical” or “identity” means that two nucleic acid sequenceshave the same sequence or a complementary sequence. Thus, “areas ofidentity” means that regions or areas of a polynucleotide or the overallpolynucleotide are identical or complementary to areas of anotherpolynucleotide or the polynucleotide.

The term “isolated” means that the material is removed from its originalenvironment (e.g., the natural environment if it is naturallyoccurring). For example, a naturally-occurring polynucleotide or enzymepresent in a living animal is not isolated, but the same polynucleotideor enzyme, separated from some or all of the coexisting materials in thenatural system, is isolated. Such polynucleotides could be part of avector and/or such polynucleotides or enzymes could be part of acomposition, and still be isolated in that such vector or composition isnot part of its natural environment.

By “isolated nucleic acid” is meant a nucleic acid, e.g., a DNA or RNAmolecule, that is not immediately contiguous with the 5′ and 3′ flankingsequences with which it normally is immediately contiguous when presentin the naturally occurring genome of the organism from which it isderived. The term thus describes, for example, a nucleic acid that isincorporated into a vector, such as a plasmid or viral vector; a nucleicacid that is incorporated into the genome of a heterologous cell (or thegenome of a homologous cell, but at a site different from that at whichit naturally occurs); and a nucleic acid that exists as a separatemolecule, e.g., a DNA fragment produced by PCR amplification orrestriction enzyme digestion, or an RNA molecule produced by in vitrotranscription. The term also describes a recombinant nucleic acid thatforms part of a hybrid gene encoding additional polypeptide sequencesthat can be used, for example, in the production of a fusion protein.

As used herein “ligand” refers to a molecule, such as a random peptideor variable segment sequence, that is recognized by a particularreceptor. As one of skill in the art will recognize, a molecule (ormacromolecular complex) can be both a receptor and a ligand. In general,the binding partner having a smaller molecular weight is referred to asthe ligand and the binding partner having a greater molecular weight isreferred to as a receptor.

“Ligation” refers to the process of forming phosphodiester bonds betweentwo double stranded nucleic acid fragments (Sambrook et al, 1982, p.146; Sambrook, 1989). Unless otherwise provided, ligation may beaccomplished using known buffers and conditions with 10 units of T4 DNAligase (“ligase”) per 0.5 μg of approximately equimolar amounts of theDNA fragments to be ligated.

As used herein, “linker” or “spacer” refers to a molecule or group ofmolecules that connects two molecules, such as a DNA binding protein anda random peptide, and serves to place the two molecules in a preferredconfiguration, e.g., so that the random peptide can bind to a receptorwith minimal steric hindrance from the DNA binding protein.

As used herein, a “molecular property to be evolved” includes referenceto molecules comprised of a polynucleotide sequence, molecules comprisedof a polypeptide sequence, and molecules comprised in part of apolynucleotide sequence and in part of a polypeptide sequence.Particularly relevant—but by no means limiting—examples of molecularproperties to be evolved include enzymatic activities at specifiedconditions, such as related to temperature; salinity; pressure; pH; andconcentration of glycerol, DMSO, detergent, &/or any other molecularspecies with which contact is made in a reaction environment. Additionalparticularly relevant—but by no means limiting—examples of molecularproperties to be evolved include stabilities—e.g. the amount of aresidual molecular property that is present after a specified exposuretime to a specified environment, such as may be encountered duringstorage.

The term “mutations” includes changes in the sequence of a wild-type orparental nucleic acid sequence or changes in the sequence of a peptide.Such mutations may be point mutations such as transitions ortransversions. The mutations may be deletions, insertions orduplications. A mutation can also be a “chimerization”, which isexemplified in a progeny molecule that is generated to contain part orall of a sequence of one parental molecule as well as part or all of asequence of at least one other parental molecule. This inventionprovides for both chimeric polynucleotides and chimeric polypeptides.

As used herein, the degenerate “N,N,G/T” nucleotide sequence represents32 possible triplets, where “N” can be A, C, G or T.

The term “naturally-occurring” as used herein as applied to the objectrefers to the fact that an object can be found in nature. For example, apolypeptide or polynucleotide sequence that is present in an organism(including viruses) that can be isolated from a source in nature andwhich has not been intentionally modified by man in the laboratory isnaturally occurring. Generally, the term naturally occurring refers toan object as present in a non-pathological (un-diseased) individual,such as would be typical for the species.

As used herein, a “nucleic acid molecule” is comprised of at least onebase or one base pair, depending on whether it is single-stranded ordouble-stranded, respectively. Furthermore, a nucleic acid molecule maybelong exclusively or chimerically to any group of nucleotide-containingmolecules, as exemplified by, but not limited to, the following groupsof nucleic acid molecules: RNA, DNA, genomic nucleic acids, non-genomicnucleic acids, naturally occurring and not naturally occurring nucleicacids, and synthetic nucleic acids. This includes, by way ofnon-limiting example, nucleic acids associated with any organelle, suchas the mitochondria, ribosomal RNA, and nucleic acid molecules comprisedchimerically of one or more components that are not naturally occurringalong with naturally occurring components.

Additionally, a “nucleic acid molecule” may contain in part one or morenon-nucleotide-based components as exemplified by, but not limited to,amino acids and sugars. Thus, by way of example, but not limitation, aribozyme that is in part nucleotide-based and in part protein-based isconsidered a “nucleic acid molecule”.

In addition, by way of example, but not limitation, a nucleic acidmolecule that is labeled with a detectable moiety, such as a radioactiveor alternatively a non-radioactive label, is likewise considered a“nucleic acid molecule”.

The terms “nucleic acid sequence coding for” or a “DNA coding sequenceof” or a “nucleotide sequence encoding” a particular enzyme—as well asother synonymous terms—refer to a DNA sequence which is transcribed andtranslated into an enzyme when placed under the control of appropriateregulatory sequences. A “promotor sequence” is a DNA regulatory regioncapable of binding RNA polymerase in a cell and initiating transcriptionof a downstream (3′ direction) coding sequence. The promoter is part ofthe DNA sequence. This sequence region has a start codon at its 3′terminus. The promoter sequence does include the minimum number of baseswhere elements necessary to initiate transcription at levels detectableabove background. However, after the RNA polymerase binds the sequenceand transcription is initiated at the start codon (3′ terminus with apromoter), transcription proceeds downstream in the 3′ direction. Withinthe promotor sequence will be found a transcription initiation site(conveniently defined by mapping with nuclease S1) as well as proteinbinding domains (consensus sequences) responsible for the binding of RNApolymerase.

The terms “nucleic acid encoding an enzyme (protein)” or “DNA encodingan enzyme (protein)” or “polynucleotide encoding an enzyme (protein)”and other synonymous terms encompasses a polynucleotide which includesonly coding sequence for the enzyme as well as a polynucleotide whichincludes additional coding and/or non-coding sequence.

In one preferred embodiment, a “specific nucleic acid molecule species”is defined by its chemical structure, as exemplified by, but not limitedto, its primary sequence. In another preferred embodiment, a specific“nucleic acid molecule species” is defined by a function of the nucleicacid species or by a function of a product derived from the nucleic acidspecies. Thus, by way of non-limiting example, a “specific nucleic acidmolecule species” may be defined by one or more activities or propertiesattributable to it, including activities or properties attributable itsexpressed product.

The instant definition of “assembling a working nucleic acid sample intoa nucleic acid library” includes the process of incorporating a nucleicacid sample into a vector-based collection, such as by ligation into avector and transformation of a host. A description of relevant vectors,hosts, and other reagents as well as specific non-limiting examplesthereof are provided hereinafter. The instant definition of “assemblinga working nucleic acid sample into a nucleic acid library” also includesthe process of incorporating a nucleic acid sample into anon-vector-based collection, such as by ligation to adaptors. Preferablythe adaptors can anneal to PCR primers to facilitate amplification byPCR.

Accordingly, in a non-limiting embodiment, a “nucleic acid library” iscomprised of a vector-based collection of one or more nucleic acidmolecules. In another preferred embodiment a “nucleic acid library” iscomprised of a non-vector-based collection of nucleic acid molecules. Inyet another preferred embodiment a “nucleic acid library” is comprisedof a combined collection of nucleic acid molecules that is in partvector-based and in part non-vector-based. Preferably, the collection ofmolecules comprising a library is searchable and separable according toindividual nucleic acid molecule species.

The present invention provides a “nucleic acid construct” oralternatively a “nucleotide construct” or alternatively a “DNAconstruct”. The term “construct” is used herein to describe a molecule,such as a polynucleotide (e.g., a phytase polynucleotide) may optionallybe chemically bonded to one or more additional molecular moieties, suchas a vector, or parts of a vector. In a specific—but by no meanslimiting-aspect, a nucleotide construct is exemplified by a DNAexpression DNA expression constructs suitable for the transformation ofa host cell.

An “oligonucleotide” (or synonymously an “oligo”) refers to either asingle stranded polydeoxynucleotide or two complementarypolydeoxynucleotide strands which may be chemically synthesized. Suchsynthetic oligonucleotides may or may not have a 5′ phosphate. Thosethat do not will not ligate to another oligonucleotide without adding aphosphate with an ATP in the presence of a kinase. A syntheticoligonucleotide will ligate to a fragment that has not beendephosphorylated. To achieve polymerase-based amplification (such aswith PCR), a “32-fold degenerate oligonucleotide that is comprised of,in series, at least a first homologous sequence, a degenerate N,N,G/Tsequence, and a second homologous sequence” is mentioned. As used inthis context, “homologous” is in reference to homology between the oligoand the parental polynucleotide that is subjected to thepolymerase-based amplification.

As used herein, the term “operably linked” refers to a linkage ofpolynucleotide elements in a functional relationship. A nucleic acid is“operably linked” when it is placed into a functional relationship withanother nucleic acid sequence. For instance, a promoter or enhancer isoperably linked to a coding sequence if it affects the transcription ofthe coding sequence. Operably linked means that the DNA sequences beinglinked are typically contiguous and, where necessary to join two proteincoding regions, contiguous and in reading frame.

A coding sequence is “operably linked to” another coding sequence whenRNA polymerase will transcribe the two coding sequences into a singlemRNA, which is then translated into a single polypeptide having aminoacids derived from both coding sequences. The coding sequences need notbe contiguous to one another so long as the expressed sequences areultimately processed to produce the desired protein.

As used herein the term “parental polynucleotide set” is a set comprisedof one or more distinct polynucleotide species. Usually this term fisused in reference to a progeny polynucleotide set which is preferablyobtained by mutagenization of the parental set, in which case the terms“parental”, “starting” and “template” are used interchangeably.

As used herein the term “physiological conditions” refers totemperature, pH, ionic strength, viscosity, and like biochemicalparameters which are compatible with a viable organism, and/or whichtypically exist intracellularly in a viable cultured yeast cell ormammalian cell. For example, the intracellular conditions in a yeastcell grown under typical laboratory culture conditions are physiologicalconditions. Suitable in vitro reaction conditions for in vitrotranscription cocktails are generally physiological conditions. Ingeneral, in vitro physiological conditions comprise 50-200 mM NaCl orKCl, pH 6.5-8.5, 20-45° C. and 0.001-10 mM divalent cation (e.g., Mg⁺⁺,Ca⁺⁺); preferably about 150 mM NaCl or KCl, pH 7.2-7.6, 5 mM divalentcation, and often include 0.01-1.0 percent nonspecific protein (e.g.,BSA). A non-ionic detergent (Tween, NP-40, Triton X-100) can often bepresent, usually at about 0.001 to 2%, typically 0.05-0.2% (v/v).Particular aqueous conditions may be selected by the practitioneraccording to conventional methods. For general guidance, the followingbuffered aqueous conditions may be applicable: 10-250 mM NaCl, 5-50 mMTris HCl, pH 5-8, with optional addition of divalent cation(s) and/ormetal chelators and/or non-ionic detergents and/or membrane fractionsand/or anti-foam agents and/or scintillants.

Standard convention (5′ to 3′) is used herein to describe the sequenceof double stranded polynucleotides.

The term “population” as used herein means a collection of componentssuch as polynucleotides, portions or polynucleotides or proteins. A“mixed population: means a collection of components which belong to thesame family of nucleic acids or proteins (i.e., are related) but whichdiffer in their sequence (i.e., are not identical) and hence in theirbiological activity.

A molecule having a “pro-form” refers to a molecule that undergoes anycombination of one or more covalent and noncovalent chemicalmodifications (e.g. glycosylation, proteolytic cleavage, dimerization oroligomerization, temperature-induced or pH-induced conformationalchange, association with a co-factor, etc.) en route to attain a moremature molecular form having a property difference (e.g. an increase inactivity) in comparison with the reference pro-form molecule. When twoor more chemical modification (e.g. two proteolytic cleavages, or aproteolytic cleavage and a deglycosylation) can be distinguished enroute to the production of a mature molecule, the reference precursormolecule may be termed a “pre-pro-form” molecule.

As used herein, the term “pseudorandom” refers to a set of sequencesthat have limited variability, such that, for example, the degree ofresidue variability at another position, but any pseudorandom positionis allowed some degree of residue variation, however circumscribed.

“Quasi-repeated units”, as used herein, refers to the repeats to bere-assorted and are by definition not identical. Indeed the method isproposed not only for practically identical encoding units produced bymutagenesis of the identical starting sequence, but also thereassortment of similar or related sequences which may divergesignificantly in some regions. Nevertheless, if the sequences containsufficient homologies to be reassorted by this approach, they can bereferred to as “quasi-repeated” units.

As used herein “random peptide library” refers to a set ofpolynucleotide sequences that encodes a set of random peptides, and tothe set of random peptides encoded by those polynucleotide sequences, aswell as the fusion proteins contain those random peptides.

As used herein, “random peptide sequence” refers to an amino acidsequence composed of two or more amino acid monomers and constructed bya stochastic or random process. A random peptide can include frameworkor scaffolding motifs, which may comprise invariant sequences.

As used herein, “receptor” refers to a molecule that has an affinity fora given ligand. Receptors can be naturally occurring or syntheticmolecules. Receptors can be employed in an unaltered state or asaggregates with other species. Receptors can be attached, covalently ornon-covalently, to a binding member, either directly or via a specificbinding substance. Examples of receptors include, but are not limitedto, antibodies, including monoclonal antibodies and antisera reactivewith specific antigenic determinants (such as on viruses, cells, orother materials), cell membrane receptors, complex carbohydrates andglycoproteins, enzymes, and hormone receptors.

“Recombinant” enzymes refer to enzymes produced by recombinant DNAtechniques, i.e., produced from cells transformed by an exogenous DNAconstruct encoding the desired enzyme. “Synthetic” enzymes are thoseprepared by chemical synthesis.

The term “related polynucleotides” means that regions or areas of thepolynucleotides are identical and regions or areas of thepolynucleotides are heterologous.

“Reductive reassortment”, as used herein, refers to the increase inmolecular diversity that is accrued through deletion (and/or insertion)events that are mediated by repeated sequences.

The following terms are used to describe the sequence relationshipsbetween two or more polynucleotides: “reference sequence,” “comparisonwindow,” “sequence identity,” “percentage of sequence identity,” and“substantial identity.”

A “reference sequence” is a defined sequence used as a basis for asequence comparison; a reference sequence may be a subset of a largersequence, for example, as a segment of a full-length cDNA or genesequence given in a sequence listing, or may comprise a complete cDNA orgene sequence. Generally, a reference sequence is at least 20nucleotides in length, frequently at least 25 nucleotides in length, andoften at least 50 nucleotides in length. Since two polynucleotides mayeach (1) comprise a sequence (i.e., a portion of the completepolynucleotide sequence) that is similar between the two polynucleotidesand (2) may further comprise a sequence that is divergent between thetwo polynucleotides, sequence comparisons between two (or more)polynucleotides are typically performed by comparing sequences of thetwo polynucleotides over a “comparison window” to identify and comparelocal regions of sequence similarity.

“Repetitive Index (RI)”, as used herein, is the average number of copiesof the quasi-repeated units contained in the cloning vector.

The term “restriction site” refers to a recognition sequence that isnecessary for the manifestation of the action of a restriction enzyme,and includes a site of catalytic cleavage. It is appreciated that a siteof cleavage may or may not be contained within a portion of arestriction site that comprises a low ambiguity sequence (i.e. asequence containing the principal determinant of the frequency ofoccurrence of the restriction site). Thus, in many cases, relevantrestriction sites contain only a low ambiguity sequence with an internalcleavage site (e.g. G/AATTC in the EcoR I site) or an immediatelyadjacent cleavage site (e.g. /CCWGG in the EcoR II site). In othercases, relevant restriction enzymes [e.g. the Eco57 I site orCTGAAG(16/14)] contain a low ambiguity sequence (e.g. the CTGAAGsequence in the Eco57 I site) with an external cleavage site (e.g. inthe N₁₆ portion of the Eco57 I site). When an enzyme (e.g. a restrictionenzyme) is said to “cleave” a polynucleotide, it is understood to meanthat the restriction enzyme catalyzes or facilitates a cleavage of apolynucleotide.

In a non-limiting aspect, a “selectable polynucleotide” is comprised ofa 5′ terminal region (or end region), an intermediate region (i.e. aninternal or central region), and a 3′ terminal region (or end region).As used in this aspect, a 5′ terminal region is a region that is locatedtowards a 5′ polynucleotide terminus (or a 5′ polynucleotide end); thusit is either partially or entirely in a 5′ half of a polynucleotide.Likewise, a 3′ terminal region is a region that is located towards a 3′polynucleotide terminus (or a 3′ polynucleotide end); thus it is eitherpartially or entirely in a 3′ half of a polynucleotide. As used in thisnon-limiting exemplification, there may be sequence overlap between anytwo regions or even among all three regions.

The term “sequence identity” means that two polynucleotide sequences areidentical (i.e., on a nucleotide-by-nucleotide basis) over the window ofcomparison. The term “percentage of sequence identity” is calculated bycomparing two optimally aligned sequences over the window of comparison,determining the number of positions at which the identical nucleic acidbase (e.g., A, T, C, G, U, or I) occurs in both sequences to yield thenumber of matched positions, dividing the number of matched positions bythe total number of positions in the window of comparison (i.e., thewindow size), and multiplying the result by 100 to yield the percentageof sequence identity. This “substantial identity”, as used herein,denotes a characteristic of a polynucleotide sequence, wherein thepolynucleotide comprises a sequence having at least 80 percent sequenceidentity, preferably at least 85 percent identity, often 90 to 95percent sequence identity, and most commonly at least 99 percentsequence identity as compared to a reference sequence of a comparisonwindow of at least 25-50 nucleotides, wherein the percentage of sequenceidentity is calculated by comparing the reference sequence to thepolynucleotide sequence which may include deletions or additions whichtotal 20 percent or less of the reference sequence over the window ofcomparison.

As known in the art “similarity” between two enzymes is determined bycomparing the amino acid sequence and its conserved amino acidsubstitutes of one enzyme to the sequence of a second enzyme. Similaritymay be determined by procedures which are well-known in the art, forexample, a BLAST program (Basic Local Alignment Search Tool at theNational Center for Biological Information).

As used herein, the term “single-chain antibody” refers to a polypeptidecomprising a V_(H) domain and a V_(L) domain in polypeptide linkage,generally liked via a spacer peptide (e.g., [Gly-Gly-Gly-Gly-Ser]_(x)),and which may comprise additional amino acid sequences at the amino-and/or carboxy-termini. For example, a single-chain antibody maycomprise a tether segment for linking to the encoding polynucleotide. Asan example, a scFv is a single-chain antibody. Single-chain antibodiesare generally proteins consisting of one or more polypeptide segments ofat least 10 contiguous amino substantially encoded by genes of theimmunoglobulin superfamily (e.g., see Williams and Barclay, 1989, pp.361-368, which is incorporated herein by reference), most frequentlyencoded by a rodent, non-human primate, avian, porcine bovine, ovine,goat, or human heavy chain or light chain gene sequence. A functionalsingle-chain antibody generally contains a sufficient portion of animmunoglobulin superfamily gene product so as to retain the property ofbinding to a specific target molecule, typically a receptor or antigen(epitope).

The members of a pair of molecules (e.g., an antibody-antigen pair or anucleic acid pair) are said to “specifically bind” to each other if theybind to each other with greater affinity than to other, non-specificmolecules. For example, an antibody raised against an antigen to whichit binds more efficiently than to a non-specific protein can bedescribed as specifically binding to the antigen. (Similarly, a nucleicacid probe can be described as specifically binding to a nucleic acidtarget if it forms a specific duplex with the target by base pairinginteractions (see above).)

“Specific hybridization” is defined herein as the formation of hybridsbetween a first polynucleotide and a second polynucleotide (e.g., apolynucleotide having a distinct but substantially identical sequence tothe first polynucleotide), wherein substantially unrelatedpolynucleotide sequences do not form hybrids in the mixture.

The term “specific polynucleotide” means a polynucleotide having certainend points and having a certain nucleic acid sequence. Twopolynucleotides wherein one polynucleotide has the identical sequence asa portion of the second polynucleotide but different ends comprises twodifferent specific polynucleotides.

“Stringent hybridization conditions” means hybridization will occur onlyif there is at least 90% identity, preferably at least 95% identity andmost preferably at least 97% identity between the sequences. SeeSambrook et al, 1989, which is hereby incorporated by reference in itsentirety.

Also included in the invention are polypeptides having sequences thatare “substantially identical” to the sequence of a phytase polypeptide,such as one of SEQ ID 1. A “substantially identical” amino acid sequenceis a sequence that differs from a reference sequence only byconservative amino acid substitutions, for example, substitutions of oneamino acid for another of the same class (e.g., substitution of onehydrophobic amino acid, such as isoleucine, valine, leucine, ormethionine, for another, or substitution of one polar amino acid foranother, such as substitution of arginine for lysine, glutamic acid foraspartic acid, or glutamine for asparagine).

Additionally a “substantially identical” amino acid sequence is asequence that differs from a reference sequence or by one or morenon-conservative substitutions, deletions, or insertions, particularlywhen such a substitution occurs at a site that is not the active sitethe molecule, and provided that the polypeptide essentially retains itsbehavioural properties. For example, one or more amino acids can bedeleted from a phytase polypeptide, resulting in modification of thestructure of the polypeptide, without significantly altering itsbiological activity. For example, amino- or carboxyl-terminal aminoacids that are not required for phytase biological activity can beremoved. Such modifications can result in the development of smalleractive phytase polypeptides.

The present invention provides a “substantially pure enzyme”. The term“substantially pure enzyme” is used herein to describe a molecule, suchas a polypeptide (e.g., a phytase polypeptide, or a fragment thereof)that is substantially free of other proteins, lipids, carbohydrates,nucleic acids, and other biological materials with which it is naturallyassociated. For example, a substantially pure molecule, such as apolypeptide, can be at least 60%, by dry weight, the molecule ofinterest. The purity of the polypeptides can be determined usingstandard methods including, e.g., polyacrylamide gel electrophoresis(e.g., SDS-PAGE), column chromatography (e.g., high performance liquidchromatography (HPLC)), and amino-terminal amino acid sequence analysis.

As used herein, “substantially pure” means an object species is thepredominant species present (i.e., on a molar basis it is more abundantthan any other individual macromolecular species in the composition),and preferably substantially purified fraction is a composition whereinthe object species comprises at least about 50 percent (on a molarbasis) of all macromolecular species present. Generally, a substantiallypure composition will comprise more than about 80 to 90 percent of allmacromolecular species present in the composition. Most preferably, theobject species is purified to essential homogeneity (contaminant speciescannot be detected in the composition by conventional detection methods)wherein the composition consists essentially of a single macromolecularspecies. Solvent species, small molecules (<500 Daltons), and elementalion species are not considered macromolecular species.

As used herein, the term “variable segment” refers to a portion of anascent peptide which comprises a random, pseudorandom, or definedkernal sequence. A variable segment” refers to a portion of a nascentpeptide which comprises a random pseudorandom, or defined kernalsequence. A variable segment can comprise both variant and invariantresidue positions, and the degree of residue variation at a variantresidue position may be limited: both options are selected at thediscretion of the practitioner. Typically, variable segments are about 5to 20 amino acid residues in length (e.g., 8 to 10), although variablesegments may be longer and may comprise antibody portions or receptorproteins, such as an antibody fragment, a nucleic acid binding protein,a receptor protein, and the like.

The term “wild-type” means that the polynucleotide does not comprise anymutations. A “wild type” protein means that the protein will be activeat a level of activity found in nature and will comprise the amino acidsequence found in nature.

The term “working”, as in “working sample”, for example, is simply asample with which one is working. Likewise, a “working molecule”, forexample is a molecule with which one is working.

DETAILED DESCRIPTION OF THE INVENTION

The invention described herein is directed to the use of repeated cyclesof reductive reassortment, recombination and selection which allow forthe directed molecular evolution of highly complex linear sequences,such as DNA, RNA or proteins thorough recombination.

In vivo shuffling of molecules can be performed utilizing the naturalproperty of cells to recombine multimers. While recombination in vivohas provided the major natural route to molecular diversity, geneticrecombination remains a relatively complex process that involves 1) therecognition of homologies; 2) strand cleavage, strand invasion, andmetabolic steps leading to the production of recombinant chiasma; andfinally 3) the resolution of chiasma into discrete recombined molecules.The formation of the chiasma requires the recognition of homologoussequences.

In a preferred embodiment, the invention relates to a method forproducing a hybrid polynucleotide from at least a first polynucleotideand a second polynucleotide. The present invention can be used toproduce a hybrid polynucleotide by introducing at least a firstpolynucleotide and a second polynucleotide which share at least oneregion of partial sequence homology into a suitable host cell. Theregions of partial sequence homology promote processes which result insequence reorganization producing a hybrid polynucleotide. The term“hybrid polynucleotide”, as used herein, is any nucleotide sequencewhich results from the method of the present invention and containssequence from at least two original polynucleotide sequences. Suchhybrid polynucleotides can result from intermolecular recombinationevents which promote sequence integration between DNA molecules. Inaddition, such hybrid polynucleotides can result from intramolecularreductive reassortment processes which utilize repeated sequences toalter a nucleotide sequence within a DNA molecule.

The invention provides a means for generating hybrid polynucleotideswhich may encode biologically active hybrid polypeptides. In one aspect,the original polynucleotides encode biologically active polypeptides.The method of the invention produces new hybrid polypeptides byutilizing cellular processes which integrate the sequence of theoriginal polynucleotides such that the resulting hybrid polynucleotideencodes a polypeptide demonstrating activities derived from the originalbiologically active polypeptides. For example, the originalpolynucleotides may encode a particular enzyme from differentmicroorganisms. An enzyme encoded by a first polynucleotide from oneorganism may, for example, function effectively under a particularenvironmental condition, e.g. high salinity. An enzyme encoded by asecond polynucleotide from a different organism may function effectivelyunder a different environmental condition, such as extremely hightemperatures. A hybrid polynucleotide containing sequences from thefirst and second original polynucleotides may encode an enzyme whichexhibits characteristics of both enzymes encoded by the originalpolynucleotides. Thus, the enzyme encoded by the hybrid polynucleotidemay function effectively under environmental conditions shared by eachof the enzymes encoded by the first and second polynucleotides, e.g.,high salinity and extreme temperatures.

Enzymes encoded by the original polynucleotides of the inventioninclude, but are not limited to; oxidoreductases, transferases,hydrolases, lyases, isomerases and ligases. A hybrid polypeptideresulting from the method of the invention may exhibit specializedenzyme activity not displayed in the original enzymes. For example,following recombination and/or reductive reassortment of polynucleotidesencoding hydrolase activities, the resulting hybrid polypeptide encodedby a hybrid polynucleotide can be screened for specialized hydrolaseactivities obtained from each of the original enzymes, i.e. the type ofbond on which the hydrolase acts and the temperature at which thehydrolase functions. Thus, for example, the hydrolase may be screened toascertain those chemical functionalities which distinguish the hybridhydrolase from the original hydrolyases, such as: (a) amide (peptidebonds), i.e. proteases; (b) ester bonds, i.e. esterases and lipases; (c)acetals, i.e., glycosidases and, for example, the temperature, pH orsalt concentration at which the hybrid polypeptide functions.

Sources of the original polynucleotides may be isolated from individualorganisms (“isolates”), collections of organisms that have been grown indefined media (“enrichment cultures”), or, most preferably, uncultivatedorganisms (“environmental samples”). The use of a culture-independentapproach to derive polynucleotides encoding novel bioactivities fromenvironmental samples is most preferable since it allows one to accessuntapped resources of biodiversity.

“Environmental libraries” are generated from environmental samples andrepresent the collective genomes of naturally occurring organismsarchived in cloning vectors that can be propagated in suitableprokaryotic hosts. Because the cloned DNA is initially extracteddirectly from environmental samples, the libraries are not limited tothe small fraction of prokaryotes that can be grown in pure culture.Additionally, a normalization of the environmental DNA present in thesesamples could allow more equal representation of the DNA from all of thespecies present in the original sample. This can dramatically increasethe efficiency of finding interesting genes from minor constituents ofthe sample which may be under-represented by several orders of magnitudecompared to the dominant species.

For example, gene libraries generated from one or more uncultivatedmicroorganisms are screened for an activity of interest. Potentialpathways encoding bioactive molecules of interest are first captured inprokaryotic cells in the form of gene expression libraries.Polynucleotides encoding activities of interest are isolated from suchlibraries and introduced into a host cell. The host cell is grown underconditions which promote recombination and/or reductive reassortmentcreating potentially active biomolecules with novel or enhancedactivities.

The microorganisms from which the polynucleotide may be prepared includeprokaryotic microorganisms, such as Eubacteria and Archaebacteria, andlower eukaryotic microorganisms such as fungi, some algae and protozoa.Polynucleotides may be isolated from environmental samples in which casethe nucleic acid may be recovered without culturing of an organism orrecovered from one or more cultured organisms. In one aspect, suchmicroorganisms may be extremophiles, such as hyperthermophiles,psychrophiles, psychrotrophs, halophiles, barophiles and acidophiles.Polynucleotides encoding enzymes isolated from extremophilicmicroorganisms are particularly preferred. Such enzymes may function attemperatures above 100° C. in terrestrial hot springs and deep seathermal vents, at temperatures below 0° C. in arctic waters, in thesaturated salt environment of the Dead Sea, at pH values around 0 incoal deposits and geothermal sulfur-rich springs, or at pH valuesgreater than 11 in sewage sludge. For example, several esterases andlipases cloned and expressed from extremophilic organisms show highactivity throughout a wide range of temperatures and pHs.

Polynucleotides selected and isolated as hereinabove described areintroduced into a suitable host cell. A suitable host cell is any cellwhich is capable of promoting recombination and/or reductivereassortment. The selected polynucleotides are preferably already in avector which includes appropriate control sequences. The host cell canbe a higher eukaryotic cell, such as a mammalian cell, or a lowereukaryotic cell, such as a yeast cell, or preferably, the host cell canbe a prokaryotic cell, such as a bacterial cell. Introduction of theconstruct into the host cell can be effected by calcium phosphatetransfection, DEAE-Dextran mediated transfection, or electroporation(Davis et al, 1986).

As representative examples of appropriate hosts, there may be mentioned:bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium;fungal cells, such as yeast; insect cells such as Drosophila S2 andSpodoptera Sf9; animal cells such as CHO, COS or Bowes melanoma;adenoviruses; and plant cells. The selection of an appropriate host isdeemed to be within the scope of those skilled in the art from theteachings herein.

With particular references to various mammalian cell culture systemsthat can be employed to express recombinant protein, examples ofmammalian expression systems include the COS-7 lines of monkey kidneyfibroblasts, described in “SV40-transformed simian cells support thereplication of early SV40 mutants” (Gluzman, 1981), and other cell linescapable of expressing a compatible vector, for example, the C127, 3T3,CHO, HeLa and BHK cell lines. Mammalian expression vectors will comprisean origin of replication, a suitable promoter and enhancer, and also anynecessary ribosome binding sites, polyadenylation site, splice donor andacceptor sites, transcriptional termination sequences, and 5′ flankingnontranscribed sequences. DNA sequences derived from the SV40 splice,and polyadenylation sites may be used to provide the requirednontranscribed genetic elements.

Host cells containing the polynucleotides of interest can be cultured inconventional nutrient media modified as appropriate for activatingpromoters, selecting transformants or amplifying genes. The cultureconditions, such as temperature, pH and the like, are those previouslyused with the host cell selected for expression, and will be apparent tothe ordinarily skilled artisan. The clones which are identified ashaving the specified enzyme activity may then be sequenced to identifythe polynucleotide sequence encoding an enzyme having the enhancedactivity.

In another aspect, it is envisioned the method of the present inventioncan be used to generate novel polynucleotides encoding biochemicalpathways from one or more operons or gene clusters or portions thereof.For example, bacteria and many eukaryotes have a coordinated mechanismfor regulating genes whose products are involved in related processes.The genes are clustered, in structures referred to as “gene clusters,”on a single chromosome and are transcribed together under the control ofa single regulatory sequence, including a single promoter whichinitiates transcription of the entire cluster. Thus, a gene cluster is agroup of adjacent genes that are either identical or related, usually asto their function. An example of a biochemical pathway encoded by geneclusters are polyketides. Polyketides are molecules which are anextremely rich source of bioactivities, including antibiotics (such astetracyclines and erythromycin), anti-cancer agents (daunomycin),immunosuppressants (FK506 and rapamycin), and veterinary products(monensin). Many polyketides (produced by polyketide synthases) arevaluable as therapeutic agents. Polyketide synthases are multifunctionalenzymes that catalyze the biosynthesis of an enormous variety of carbonchains differing in length and patterns of functionality andcyclization. Polyketide synthase genes fall into gene clusters and atleast one type (designated type I) of polyketide synthases have largesize genes and enzymes, complicating genetic manipulation and in vitrostudies of these genes/proteins.

The ability to select and combine desired components from a library ofpolyketides, or fragments thereof, and postpolyketide biosynthesis genesfor generation of novel polyketides for study is appealing. The methodof the present invention makes it possible to facilitate the productionof novel polyketide synthases through intermolecular recombination.

Preferably, gene cluster DNA can be isolated from different organismsand ligated into vectors, particularly vectors containing expressionregulatory sequences which can control and regulate the production of adetectable protein or protein-related array activity from the ligatedgene clusters. Use of vectors which have an exceptionally large capacityfor exogenous DNA introduction are particularly appropriate for use withsuch gene clusters and are described by way of example herein to includethe f-factor (or fertility factor) of E. coli. This f-factor of E. coliis a plasmid which affect high-frequency transfer of itself duringconjugation and is ideal to achieve and stably propagate large DNAfragments, such as gene clusters from mixed microbial samples. Onceligated into an appropriate vector, two or more vectors containingdifferent polyketide synthase gene clusters can be introduced into asuitable host cell. Regions of partial sequence homology shared by thegene clusters will promote processes which result in sequencereorganization resulting in a hybrid gene cluster. The novel hybrid genecluster can then be screened for enhanced activities not found in theoriginal gene clusters.

Therefore, in a preferred embodiment, the present invention relates to amethod for producing a biologically active hybrid polypeptide andscreening such a polypeptide for enhanced activity by:

1) introducing at least a first polynucleotide in operable linkage and asecond polynucleotide in operable linkage, said at least firstpolynucleotide and second polynucleotide sharing at least one region ofpartial sequence homology, into a suitable host cell;

2) growing the host cell under conditions which promote sequencereorganization resulting in a hybrid polynucleotide in operable linkage;

3) expressing a hybrid polypeptide encoded by the hybrid polynucleotide;

4) screening the hybrid polypeptide under conditions which promoteidentification of enhanced biological activity; and

5) isolating the a polynucleotide encoding the hybrid polypeptide.

Methods for screening for various enzyme activities are known to thoseof skill in the art and discussed throughout the present specification.Such methods may be employed when isolating the polypeptides andpolynucleotides of the present invention.

As representative examples of expression vectors which may be used theremay be mentioned viral particles, baculovirus, phage, plasmids,phagemids, cosmids, fosmids, bacterial artificial chromosomes, viral DNA(e.g. vaccinia, adenovirus, foul pox virus, pseudorabies and derivativesof SV40), P1-based artificial chromosomes, yeast plasmids, yeastartificial chromosomes, and any other vectors specific for specifichosts of interest (such as bacillus, aspergillus and yeast). Thus, forexample, the DNA may be included in any one of a variety of expressionvectors for expressing a polypeptide. Such vectors include chromosomal,nonchromosomal and synthetic DNA sequences. Large numbers of suitablevectors are known to those of skill in the art, and are commerciallyavailable. The following vectors are provided by way of example;Bacterial: pQE vectors (Qiagen), pBluescript plasmids, pNH vectors,(lambda-ZAP vectors (Stratagene); ptrc99a, pKK223-3, pDR540, pRIT2T(Pharmacia); Eukaryotic: pXT1, pSG5 (Stratagene), pSVK3, pBPV, pMSG,pSVLSV40 (Pharmacia). However, any other plasmid or other vector may beused as long as they are replicable and viable in the host. Low copynumber or high copy number vectors may be employed with the presentinvention.

A preferred type of vector for use in the present invention contains anf-factor origin replication. The f-factor (or fertility factor) in E.coli is a plasmid which effects high frequency transfer of itself duringconjugation and less frequent transfer of the bacterial chromosomeitself. A particularly preferred embodiment is to use cloning vectors,referred to as “fosmids” or bacterial artificial chromosome (BAC)vectors. These are derived from E. coli f-factor which is able to stablyintegrate large segments of genomic DNA. When integrated with DNA from amixed uncultured environmental sample, this makes it possible to achievelarge genomic fragments in the form of a stable “environmental DNAlibrary.”

Another preferred type of vector for use in the present invention is acosmid vector. Cosmid vectors were originally designed to clone andpropagate large segments of genomic DNA. Cloning into cosmid vectors isdescribed in detail in “Molecular Cloning: A laboratory Manual”(Sambrook et al, 1989).

The DNA sequence in the expression vector is operatively linked to anappropriate expression control sequence(s) (promoter) to direct RNAsynthesis. Particular named bacterial promoters include lacI, lacZ, T3,T7, gpt, lambda P_(R), P_(L) and trp. Eukaryotic promoters include CMVimmediate early, HSV thymidine kinase, early and late SV40, LTRs fromretrovirus, and mouse metallothionein-I. Selection of the appropriatevector and promoter is well within the level of ordinary skill in theart. The expression vector also contains a ribosome binding site fortranslation initiation and a transcription terminator. The vector mayalso include appropriate sequences for amplifying expression. Promoterregions can be selected from any desired gene using CAT (chloramphenicoltransferase) vectors or other vectors with selectable markers.

In addition, the expression vectors preferably contain one or moreselectable marker genes to provide a phenotypic trait for selection oftransformed host cells such as dihydrofolate reductase or neomycinresistance for eukaryotic cell culture, or such as tetracycline orampicillin resistance in E. coli.

Generally, recombinant expression vectors will include origins ofreplication and selectable markers permitting transformation of the hostcell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiaeTRP1 gene, and a promoter derived from a highly-expressed gene to directtranscription of a downstream structural sequence. Such promoters can bederived from operons encoding glycolytic enzymes such as3-phosphoglycerate kinase (PGK), α-factor, acid phosphatase, or heatshock proteins, among others. The heterologous structural sequence isassembled in appropriate phase with translation initiation andtermination sequences, and preferably, a leader sequence capable ofdirecting secretion of translated protein into the periplasmic space orextracellular medium.

The cloning strategy permits expression via both vector driven andendogenous promoters; vector promotion may be important with expressionof genes whose endogenous promoter will not function in E. coli.

The DNA isolated or derived from microorganisms can preferably beinserted into a vector or a plasmid prior to probing for selected DNA.Such vectors or plasmids are preferably those containing expressionregulatory sequences, including promoters, enhancers and the like. Suchpolynucleotides can be part of a vector and/or a composition and stillbe isolated, in that such vector or composition is not part of itsnatural environment. Particularly preferred phage or plasmid and methodsfor introduction and packaging into them are described in detail in theprotocol set forth herein.

The selection of the cloning vector depends upon the approach taken, forexample, the vector can be any cloning vector with an adequate capacityfor multiply repeated copies of a sequence, or multiple sequences thatcan be successfully transformed and selected in a host cell. One exampleof such a vector is described in “Polycos vectors: a system forpackaging filamentous phage and phagemid vectors using lambda phagepackaging extracts” (Alting-Mecs and Short, 1993).Propagation/maintenance can be by an antibiotic resistance carried bythe cloning vector. After a period of growth, the naturally abbreviatedmolecules are recovered and identified by size fractionation on a gel orcolumn, or amplified directly. The cloning vector utilized may contain aselectable gene that is disrupted by the insertion of the lengthyconstruct. As reductive reassortment progresses, the number of repeatedunits is reduced and the interrupted gene is again expressed and henceselection for the processed construct can be applied. The vector may bean expression/selection vector which will allow for the selection of anexpressed product possessing desirable biologically properties. Theinsert may be positioned downstream of a functional promotor and thedesirable property screened by appropriate means.

In vivo reassortment is focused on “inter-molecular” processescollectively referred to as “recombination” which in bacteria, isgenerally viewed as a “RecA-dependent” phenomenon. The present inventioncan rely on recombination processes of a host cell to recombine andre-assort sequences, or the cells' ability to mediate reductiveprocesses to decrease the complexity of quasi-repeated sequences in thecell by deletion. This process of “reductive reassortment” occurs by an“intra-molecular”, RecA-independent process.

Therefore, in another aspect of the present invention, novelpolynucleotides can be generated by the process of reductivereassortment. The method involves the generation of constructscontaining consecutive sequences (original encoding sequences), theirinsertion into an appropriate vector, and their subsequent introductioninto an appropriate host cell. The reassortment of the individualmolecular identities occurs by combinatorial processes between theconsecutive sequences in the construct possessing regions of homology,or between quasi-repeated units. The reassortment process recombinesand/or reduces the complexity and extent of the repeated sequences, andresults in the production of novel molecular species. Various treatmentsmay be applied to enhance the rate of reassortment. These could includetreatment with ultra-violet light, or DNA damaging chemicals, and/or theuse of host cell lines displaying enhanced levels of “geneticinstability”. Thus the reassortment process may involve homologousrecombination or the natural property of quasi-repeated sequences todirect their own evolution.

Repeated or “quasi-repeated” sequences play a role in geneticinstability. In the present invention, “quasi-repeats” are repeats thatare not restricted to their original unit structure. Quasi-repeatedunits can be presented as an array of sequences in a construct;consecutive units of similar sequences. Once ligated, the junctionsbetween the consecutive sequences become essentially invisible and thequasi-repetitive nature of the resulting construct is now continuous atthe molecular level. The deletion process the cell performs to reducethe complexity of the resulting construct operates between thequasi-repeated sequences. The quasi-repeated units provide a practicallylimitless repertoire of templates upon which slippage events can occur.The constructs containing the quasi-repeats thus effectively providesufficient molecular elasticity that deletion (and potentiallyinsertion) events can occur virtually anywhere within thequasi-repetitive units.

When the quasi-repeated sequences are all ligated in the sameorientation, for instance head to tail or vice versa, the cell cannotdistinguish individual units. Consequently, the reductive process canoccur throughout the sequences. In contrast, when for example, the unitsare presented head to head, rather than head to tail, the inversiondelineates the endpoints of the adjacent unit so that deletion formationwill favor the loss of discrete units. Thus, it is preferable with thepresent method that the sequences are in the same orientation. Randomorientation of quasi-repeated sequences will result in the loss ofreassortment efficiency, while consistent orientation of the sequenceswill offer the highest efficiency. However, while having fewer of thecontiguous sequences in the same orientation decreases the efficiency,it may still provide sufficient elasticity for the effective recovery ofnovel molecules. Constructs can be made with the quasi-repeatedsequences in the same orientation to allow higher efficiency.

Sequences can be assembled in a head to tail orientation using any of avariety of methods, including the following:

a) Primers that include a poly-A head and poly-T tail which when madesingle-stranded would provide orientation can be utilized. This isaccomplished by having the first few bases of the primers made from RNAand hence easily removed RNAseH.

b) Primers that include unique restriction cleavage sites can beutilized. Multiple sites, a battery of unique sequences, and repeatedsynthesis and ligation steps would be required.

c) The inner few bases of the primer could be thiolated and anexonuclease used to produce properly tailed molecules.

The recovery of the re-assorted sequences relies on the identificationof cloning vectors with a reduced RI. The re-assorted encoding sequencescan then be recovered by amplification. The products are re-cloned andexpressed. The recovery of cloning vectors with reduced RI can beeffected by:

1) The use of vectors only stably maintained when the construct isreduced in complexity.

2) The physical recovery of shortened vectors by physical procedures. Inthis case, the cloning vector would be recovered using standard plasmidisolation procedures and size fractionated on either an agarose gel, orcolumn with a low molecular weight cut off utilizing standardprocedures.

3) The recovery of vectors containing interrupted genes which can beselected when insert size decreases.

4) The use of direct selection techniques with an expression vector andthe appropriate selection.

Encoding sequences (for example, genes) from related organisms maydemonstrate a high degree of homology and encode quite diverse proteinproducts. These types of sequences are particularly useful in thepresent invention as quasi-repeats. However, while the examplesillustrated below demonstrate the reassortment of nearly identicaloriginal encoding sequences (quasi-repeats), this process is not limitedto such nearly identical repeats.

The following example demonstrates the method of the invention. Encodingnucleic acid sequences (quasi-repeats) derived from three (3) uniquespecies are depicted. Each sequence encodes a protein with a distinctset of properties. Each of the sequences differs by a single or a fewbase pairs at a unique position in the sequence which are designated“A”, “B” and “C”. The quasi-repeated sequences are separately orcollectively amplified and ligated into random assemblies such that allpossible permutations and combinations are available in the populationof ligated molecules. The number of quasi-repeat units can be controlledby the assembly conditions. The average number of quasi-repeated unitsin a construct is defined as the repetitive index (RI).

Once formed, the constructs may, or may not be size fractionated on anagarose gel according to published protocols, inserted into a cloningvector, and transfected into an appropriate host cell. The cells arethen propagated and “reductive reassortment” is effected. The rate ofthe reductive reassortment process may be stimulated by the introductionof DNA damage if desired. Whether the reduction in RI is mediated bydeletion formation between repeated sequences by an “intra-molecular”mechanism, or mediated by recombination-like events through“inter-molecular” mechanisms is immaterial. The end result is areassortment of the molecules into all possible combinations.

Optionally, the method comprises the additional step of screening thelibrary members of the shuffled pool to identify individual shuffledlibrary members having the ability to bind or otherwise interact (e.g.,such as catalytic antibodies) with a predetermined macromolecule, suchas for example a proteinaceous receptor, peptide oligosaccharide, viron,or other predetermined compound or structure.

The displayed polypeptides, antibodies, peptidomimetic antibodies, andvariable region sequences that are identified from such libraries can beused for therapeutic, diagnostic, research and related purposes (e.g.,catalysts, solutes for increasing osmolarity of an aqueous solution, andthe like), and/or can be subjected to one or more additional cycles ofshuffling and/or affinity selection. The method can be modified suchthat the step of selecting for a phenotypic characteristic can be otherthan of binding affinity for a predetermined molecule (e.g., forcatalytic activity, stability oxidation resistance, drug resistance, ordetectable phenotype conferred upon a host cell).

The present invention provides a method for generating libraries ofdisplayed antibodies suitable for affinity interactions screening. Themethod comprises (1) obtaining first a plurality of selected librarymembers comprising a displayed antibody and an associated polynucleotideencoding said displayed antibody, and obtaining said associatedpolynucleotide encoding for said displayed antibody and obtaining saidassociated polynucleotides or copies thereof, wherein said associatedpolynucleotides comprise a region of substantially identical variableregion framework sequence, and (2) introducing said polynucleotides intoa suitable host cell and growing the cells under conditions whichpromote recombination and reductive reassortment resulting in shuffledpolynucleotides. CDR combinations comprised by the shuffled pool are notpresent in the first plurality of selected library members, saidshuffled pool composing a library of displayed antibodies comprising CDRpermutations and suitable for affinity interaction screening.Optionally, the shuffled pool is subjected to affinity screening toselect shuffled library members which bind to a predetermined epitope(antigen) and thereby selecting a plurality of selected shuffled librarymembers. Further, the plurality of selectively shuffled library memberscan be shuffled and screened iteratively, from 1 to about 1000 cycles oras desired until library members having a desired binding affinity areobtained.

In another aspect of the invention, it is envisioned that prior to orduring recombination or reassortment, polynucleotides generated by themethod of the present invention can be subjected to agents or processeswhich promote the introduction of mutations into the originalpolynucleotides. The introduction of such mutations would increase thediversity of resulting hybrid polynucleotides and polypeptides encodedtherefrom. The agents or processes which promote mutagenesis caninclude, but are not limited to: (+)-CC-1065, or a synthetic analog suchas (+)-CC-1065-(N3-Adenine, see Sun and Hurley, 1992); an N-acelylatedor deacetylated 4′-fluro-4-aminobiphenyl adduct capable of inhibitingDNA synthesis (see, for example, van de Poll et al, 1992); or aN-acetylated or deacetylated 4-aminobiphenyl adduct capable ofinhibiting DNA synthesis (see also, van de Poll et al, 1992, pp.751-758); trivalent chromium, a trivalent chromium salt, a polycyclicaromatic hydrocarbon (“PAH”) DNA adduct capable of inhibiting DNAreplication, such as 7-bromomethyl-benz[a]anthracene (“BMA”),tris(2,3-dibromopropyl)phosphate (“Tris-BP”),1,2-dibromo-3-chloropropane (“DBCP”), 2-bromoacrolein (2BA),benzo[a]pyrene-7,8-dihydrodiol-9-10-epoxide (“BPDE”), a platinum(II)halogen salt, N-hydroxy-2-amino-3-methylimidazo[4,5-f]-quinoline(“N-hydroxy-IQ”), andN-hydroxy-2-amino-1-methyl-6-phenylimidazo[4,5-f]-pyridine(“N-hydroxy-PhIP”). Especially preferred “means for slowing or haltingPCR amplification consist of UV light (+)-CC-1065 and(+)-CC-1065-(N3-Adenine). Particularly encompassed means are DNA adductsor polynucleotides comprising the DNA adducts from the polynucleotidesor polynucleotides pool, which can be released or removed by a processincluding heating the solution comprising the polynucleotides prior tofurther processing.

In another aspect the present invention is directed to a method ofproducing recombinant proteins having biological activity by treating asample comprising double-stranded template polynucleotides encoding awild-type protein under conditions according to the present inventionwhich provide for the production of hybrid or re-assortedpolynucleotides.

The invention also provides the use of polynucleotide shuffling toshuffle a population of viral genes (e.g., capsid proteins, spikeglycoproteins, polymerases, and proteases) or viral genomes (e.g.,paramyxoviridae, orthomyxoviridae, herpesviruses, retroviruses,reoviruses and rhinoviruses). In an embodiment, the invention provides amethod for shuffling sequences encoding all or portions of immunogenicviral proteins to generate novel combinations of epitopes as well asnovel epitopes created by recombination; such shuffled viral proteinsmay comprise epitopes or combinations of epitopes as well as novelepitopes created by recombination; such shuffled viral proteins maycomprise epitopes or combinations of epitopes which are likely to arisein the natural environment as a consequence of viral evolution; (e.g.,such as recombination of influenza virus strains).

The invention also provides a method suitable for shufflingpolynucleotide sequences for generating gene therapy vectors andreplication-defective gene therapy constructs, such as may be used forhuman gene therapy, including but not limited to vaccination vectors forDNA-based vaccination, as well as anti-neoplastic gene therapy and othergeneral therapy formats.

In the polypeptide notation used herein, the left-hand direction is theamino terminal direction and the right-hand direction is thecarboxy-terminal direction, in accordance with standard usage andconvention. Similarly, unless specified otherwise, the left-hand end ofsingle-stranded polynucleotide sequences is the 5′ end; the left-handdirection of double-stranded polynucleotide sequences is referred to asthe 5′ direction. The direction of 5′ to 3′ addition of nascent RNAtranscripts is referred to as the transcription direction; sequenceregions on the DNA strand having the same sequence as the RNA and whichare 5′ to the 5′ end of the RNA transcript are referred to as “upstreamsequences”; sequence regions on the DNA strand having the same sequenceas the RNA and which are 3′ to the 3′ end of the coding RNA transcriptare referred to as “downstream sequences”.

Methodology

Nucleic acid shuffling is a method for in vitro or in vivo homologousrecombination of pools of shorter or smaller polynucleotides to producea polynucleotide or polynucleotides. Mixtures of related nucleic acidsequences or polynucleotides are subjected to sexual PCR to providerandom polynucleotides, and reassembled to yield a library or mixedpopulation of recombinant hybrid nucleic acid molecules orpolynucleotides.

In contrast to cassette mutagenesis, only shuffling and error-prone PCRallow one to mutate a pool of sequences blindly (without sequenceinformation other than primers).

The advantage of the mutagenic shuffling of this invention overerror-prone PCR alone for repeated selection can best be explained withan example from antibody engineering. Consider DNA shuffling as comparedwith error-prone PCR (not sexual PCR). The initial library of selectedpooled sequences can consist of related sequences of diverse origin(i.e. antibodies from naive mRNA) or can be derived by any type ofmutagenesis (including shuffling) of a single antibody gene. Acollection of selected complementarity determining regions (“CDRs”) isobtained after the first round of affinity selection. In the diagram thethick CDRs confer onto the antibody molecule increased affinity for theantigen. Shuffling allows the free combinatorial association of all ofthe CDR1s with all of the CDR2s with all of the CDR3s, for example.

This method differs from error-prone PCR, in that it is an inverse chainreaction. In error-prone PCR, the number of polymerase start sites andthe number of molecules grows exponentially. However, the sequence ofthe polymerase start sites and the sequence of the molecules remainsessentially the same. In contrast, in nucleic acid reassembly orshuffling of random polynucleotides the number of start sites and thenumber (but not size) of the random polynucleotides decreases over time.For polynucleotides derived from whole plasmids the theoretical endpointis a single, large concatemeric molecule.

Since cross-overs occur at regions of homology, recombination willprimarily occur between members of the same sequence family. Thisdiscourages combinations of CDRs that are grossly incompatible (e.g.,directed against different epitopes of the same antigen). It iscontemplated that multiple families of sequences can be shuffled in thesame reaction. Further, shuffling generally conserves the relativeorder, such that, for example, CDR1 will not be found in the position ofCDR2.

Rare shufflants will contain a large number of the best (eg. highestaffinity) CDRs and these rare shufflants may be selected based on theirsuperior affinity.

CDRs from a pool of 100 different selected antibody sequences can bepermutated in up to 1006 different ways. This large number ofpermutations cannot be represented in a single library of DNA sequences.Accordingly, it is contemplated that multiple cycles of DNA shufflingand selection may be required depending on the length of the sequenceand the sequence diversity desired.

Error-prone PCR, in contrast, keeps all the selected CDRs in the samerelative sequence, generating a much smaller mutant cloud.

The template polynucleotide which may be used in the methods of thisinvention may be DNA or RNA. It may be of various lengths depending onthe size of the gene or shorter or smaller polynucleotide to berecombined or reassembled. Preferably, the template polynucleotide isfrom 50 bp to 50 kb. It is contemplated that entire vectors containingthe nucleic acid encoding the protein of interest can be used in themethods of this invention, and in fact have been successfully used.

The template polynucleotide may be obtained by amplification using thePCR reaction (U.S. Pat. No. 4,683,202 and U.S. Pat. No. 4,683,195) orother amplification or cloning methods. However, the removal of freeprimers from the PCR products before subjecting them to pooling of thePCR products and sexual PCR may provide more efficient results. Failureto adequately remove the primers from the original pool before sexualPCR can lead to a low frequency of crossover clones.

The template polynucleotide often should be double-stranded. Adouble-stranded nucleic acid molecule is recommended to ensure thatregions of the resulting single-stranded polynucleotides arecomplementary to each other and thus can hybridize to form adouble-stranded molecule.

It is contemplated that single-stranded or double-stranded nucleic acidpolynucleotides having regions of identity to the templatepolynucleotide and regions of heterology to the template polynucleotidemay be added to the template polynucleotide, at this step. It is alsocontemplated that two different but related polynucleotide templates canbe mixed at this step.

The double-stranded polynucleotide template and any added double- orsingle-stranded polynucleotides are subjected to sexual PCR whichincludes slowing or halting to provide a mixture of from about 5 bp to 5kb or more. Preferably the size of the random polynucleotides is fromabout 10 bp to 1000 bp, more preferably the size of the polynucleotidesis from about 20 bp to 500 bp.

Alternatively, it is also contemplated that double-stranded nucleic acidhaving multiple nicks may be used in the methods of this invention. Anick is a break in one strand of the double-stranded nucleic acid. Thedistance between such nicks is preferably 5 bp to 5 kb, more preferablybetween 10 bp to 1000 bp. This can provide areas of self-priming toproduce shorter or smaller polynucleotides to be included with thepolynucleotides resulting from random primers, for example.

The concentration of any one specific polynucleotide will not be greaterthan 1% by weight of the total polynucleotides, more preferably theconcentration of any one specific nucleic acid sequence will not begreater than 0.1% by weight of the total nucleic acid.

The number of different specific polynucleotides in the mixture will beat least about 100, preferably at least about 500, and more preferablyat least about 1000.

At this step single-stranded or double-stranded polynucleotides, eithersynthetic or natural, may be added to the random double-stranded shorteror smaller polynucleotides in order to increase the heterogeneity of themixture of polynucleotides.

It is also contemplated that populations of double-stranded randomlybroken polynucleotides may be mixed or combined at this step with thepolynucleotides from the sexual PCR process and optionally subjected toone or more additional sexual PCR cycles.

Where insertion of mutations into the template polynucleotide isdesired, single-stranded or double-stranded polynucleotides having aregion of identity to the template polynucleotide and a region ofheterology to the template polynucleotide may be added in a 20 foldexcess by weight as compared to the total nucleic acid, more preferablythe single-stranded polynucleotides may be added in a 10 fold excess byweight as compared to the total nucleic acid.

Where a mixture of different but related template polynucleotides isdesired, populations of polynucleotides from each of the templates maybe combined at a ratio of less than about 1:100, more preferably theratio is less than about 1:40. For example, a backcross of the wild-typepolynucleotide with a population of mutated polynucleotide may bedesired to eliminate neutral mutations (e.g., mutations yielding aninsubstantial alteration in the phenotypic property being selected for).In such an example, the ratio of randomly provided wild-typepolynucleotides which may be added to the randomly provided sexual PCRcycle hybrid polynucleotides is approximately 1:1 to about 100:1, andmore preferably from 1:1 to 40:1.

The mixed population of random polynucleotides are denatured to formsingle-stranded polynucleotides and then re-annealed. Only thosesingle-stranded polynucleotides having regions of homology with othersingle-stranded polynucleotides will re-anneal.

The random polynucleotides may be denatured by heating. One skilled inthe art could determine the conditions necessary to completely denaturethe double-stranded nucleic acid. Preferably the temperature is from 80°C. to 100° C., more preferably the temperature is from 90° C. to 96° C.other methods which may be used to denature the polynucleotides includepressure (36) and pH.

The polynucleotides may be re-annealed by cooling. Preferably thetemperature is from 20° C. to 75° C., more preferably the temperature isfrom 40° C. to 65° C. If a high frequency of crossovers is needed basedon an average of only 4 consecutive bases of homology, recombination canbe forced by using a low annealing temperature, although the processbecomes more difficult. The degree of renaturation which occurs willdepend on the degree of homology between the population ofsingle-stranded polynucleotides.

Renaturation can be accelerated by the addition of polyethylene glycol(“PEG”) or salt. The salt concentration is preferably from 0 mM to 200mM, more preferably the salt concentration is from 10 mM to 100 mm. Thesalt may be KCl or NaCl. The concentration of PEG is preferably from 0%to 20%, more preferably from 5% to 10%.

The annealed polynucleotides are next incubated in the presence of anucleic acid polymerase and dNTP's (i.e. dATP, dCTP, DGTP and dTTP). Thenucleic acid polymerase may be the Klenow fragment, the Taq polymeraseor any other DNA polymerase known in the art.

The approach to be used for the assembly depends on the minimum degreeof homology that should still yield crossovers. If the areas of identityare large, Taq polymerase can be used with an annealing temperature ofbetween 45-65° C. If the areas of identity are small, Klenow polymerasecan be used with an annealing temperature of between 20-30° C. Oneskilled in the art could vary the temperature of annealing to increasethe number of cross-overs achieved.

The polymerase may be added to the random polynucleotides prior toannealing, simultaneously with annealing or after annealing.

The cycle of denaturation, renaturation and incubation in the presenceof polymerase is referred to herein as shuffling or reassembly of thenucleic acid. This cycle is repeated for a desired number of times.Preferably the cycle is repeated from 2 to 50 times, more preferably thesequence is repeated from 10 to 40 times.

The resulting nucleic acid is a larger double-stranded polynucleotide offrom about 50 bp to about 100 kb, preferably the larger polynucleotideis from 500 bp to 50 kb.

This larger polynucleotides may contain a number of copies of apolynucleotide having the same size as the template polynucleotide intandem. This concatemeric polynucleotide is then denatured into singlecopies of the template polynucleotide. The result will be a populationof polynucleotides of approximately the same size as the templatepolynucleotide. The population will be a mixed population where singleor double-stranded polynucleotides having an area of identity and anarea of heterology have been added to the template polynucleotide priorto shuffling.

These polynucleotides are then cloned into the appropriate vector andthe ligation mixture used to transform bacteria.

It is contemplated that the single polynucleotides may be obtained fromthe larger concatemeric polynucleotide by amplification of the singlepolynucleotide prior to cloning by a variety of methods including PCR(U.S. Pat. No. 4,683,195 and U.S. Pat. No. 4,683,202), rather than bydigestion of the concatemer.

The vector used for cloning is not critical provided that it will accepta polynucleotide of the desired size. If expression of the particularpolynucleotide is desired, the cloning vehicle should further comprisetranscription and translation signals next to the site of insertion ofthe polynucleotide to allow expression of the polynucleotide in the hostcell. Preferred vectors include the pUC series and the pBR series ofplasmids.

The resulting bacterial population will include a number of recombinantpolynucleotides having random mutations. This mixed population may betested to identify the desired recombinant polynucleotides. The methodof selection will depend on the polynucleotide desired.

For example, if a polynucleotide which encodes a protein with increasedbinding efficiency to a ligand is desired, the proteins expressed byeach of the portions of the polynucleotides in the population or librarymay be tested for their ability to bind to the ligand by methods knownin the art (i e panning, affinity chromatography). If a polynucleotidewhich encodes for a protein with increased drug resistance is desired,the proteins expressed by each of the polynucleotides in the populationor library may be tested for their ability to confer drug resistance tothe host organism. One skilled in the art, given knowledge of thedesired protein, could readily test the population to identifypolynucleotides which confer the desired properties onto the protein.

It is contemplated that one skilled in the art could use a phage displaysystem in which fragments of the protein are expressed as fusionproteins on the phage surface (Pharmacia, Milwaukee Wis.). Therecombinant DNA molecules are cloned into the phage DNA at a site whichresults in the transcription of a fusion protein a portion of which isencoded by the recombinant DNA molecule. The phage containing therecombinant nucleic acid molecule undergoes replication andtranscription in the cell. The leader sequence of the fusion proteindirects the transport of the fusion protein to the tip of the phageparticle. Thus the fusion protein which is partially encoded by therecombinant DNA molecule is displayed on the phage particle fordetection and selection by the methods described above.

It is further contemplated that a number of cycles of nucleic acidshuffling may be conducted with polynucleotides from a sub-population ofthe first population, which sub-population contains DNA encoding thedesired recombinant protein. In this manner, proteins with even higherbinding affinities or enzymatic activity could be achieved.

It is also contemplated that a number of cycles of nucleic acidshuffling may be conducted with a mixture of wild-type polynucleotidesand a sub-population of nucleic acid from the first or subsequent roundsof nucleic acid shuffling in order to remove any silent mutations fromthe sub-population.

Any source of nucleic acid, in purified form can be utilized as thestarting nucleic acid. Thus the process may employ DNA or RNA includingmessenger RNA, which DNA or RNA may be single or double stranded. Inaddition, a DNA-RNA hybrid which contains one strand of each may beutilized. The nucleic acid sequence may be of various lengths dependingon the size of the nucleic acid sequence to be mutated. Preferably thespecific nucleic acid sequence is from 50 to 50000 base pairs. It iscontemplated that entire vectors containing the nucleic acid encodingthe protein of interest may be used in the methods of this invention.

The nucleic acid may be obtained from any source, for example, fromplasmids such a pBR322, from cloned DNA or RNA or from natural DNA orRNA from any source including bacteria, yeast, viruses and higherorganisms such as plants or animals. DNA or RNA may be extracted fromblood or tissue material. The template polynucleotide may be obtained byamplification using the polynucleotide chain reaction (PCR, see U.S.Pat. No. 4,683,202 and U.S. Pat. No. 4,683,195). Alternatively, thepolynucleotide may be present in a vector present in a cell andsufficient nucleic acid may be obtained by culturing the cell andextracting the nucleic acid from the cell by methods known in the art.

Any specific nucleic acid sequence can be used to produce the populationof hybrids by the present process. It is only necessary that a smallpopulation of hybrid sequences of the specific nucleic acid sequenceexist or be created prior to the present process.

The initial small population of the specific nucleic acid sequenceshaving mutations may be created by a number of different methods.Mutations may be created by error-prone PCR. Error-prone PCR useslow-fidelity polymerization conditions to introduce a low level of pointmutations randomly over a long sequence. Alternatively, mutations can beintroduced into the template polynucleotide by oligonucleotide-directedmutagenesis. In oligonucleotide-directed mutagenesis, a short sequenceof the polynucleotide is removed from the polynucleotide usingrestriction enzyme digestion and is replaced with a syntheticpolynucleotide in which various bases have been altered from theoriginal sequence. The polynucleotide sequence can also be altered bychemical mutagenesis. Chemical mutagens include, for example, sodiumbisulfite, nitrous acid, hydroxylamine, hydrazine or formic acid. otheragents which are analogues of nucleotide precursors includenitrosoguanidine, 5-bromouracil, 2-aminopurine, or acridine. Generally,these agents are added to the PCR reaction in place of the nucleotideprecursor thereby mutating the sequence. Intercalating agents such asproflavine, acriflavine, quinacrine and the like can also be used.Random mutagenesis of the polynucleotide sequence can also be achievedby irradiation with X-rays or ultraviolet light. Generally, plasmidpolynucleotides so mutagenized are introduced into E. coli andpropagated as a pool or library of hybrid plasmids.

Alternatively the small mixed population of specific nucleic acids maybe found in nature in that they may consist of different alleles of thesame gene or the same gene from different related species (i.e., cognategenes). Alternatively, they may be related DNA sequences found withinone species, for example, the immunoglobulin genes.

Once the mixed population of the specific nucleic acid sequences isgenerated, the polynucleotides can be used directly or inserted into anappropriate cloning vector, using techniques well-known in, the art.

The choice of vector depends on the size of the polynucleotide sequenceand the host cell to be employed in the methods of this invention. Thetemplates of this invention may be plasmids, phages, cosmids, phagemids,viruses (e.g., retroviruses, parainfluenzavirus, herpesviruses,reoviruses, paramyxoviruses, and the like), or selected portions thereof(e.g., coat protein, spike glycoprotein, capsid protein). For example,cosmids and phagemids are preferred where the specific nucleic acidsequence to be mutated is larger because these vectors are able tostably propagate large polynucleotides.

If the mixed population of the specific nucleic acid sequence is clonedinto a vector it can be clonally amplified by inserting each vector intoa host cell and allowing the host cell to amplify the vector. This isreferred to as clonal amplification because while the absolute number ofnucleic acid sequences increases, the number of hybrids does notincrease. Utility can be readily determined by screening expressedpolypeptides.

The DNA shuffling method of this invention can be performed blindly on apool of unknown sequences. By adding to the reassembly mixtureoligonucleotides (with ends that are homologous to the sequences beingreassembled) any sequence mixture can be incorporated at any specificposition into another sequence mixture. Thus, it is contemplated thatmixtures of synthetic oligonucleotides, PCR polynucleotides or evenwhole genes can be mixed into another sequence library at definedpositions. The insertion of one sequence (mixture) is independent fromthe insertion of a sequence in another part of the template. Thus, thedegree of recombination, the homology required, and the diversity of thelibrary can be independently and simultaneously varied along the lengthof the reassembled DNA.

This approach of mixing two genes may be useful for the humanization ofantibodies from murine hybridomas. The approach of mixing two genes orinserting alternative sequences into genes may be useful for anytherapeutically used protein, for example, interleukin I, antibodies,tPA and growth hormone. The approach may also be useful in any nucleicacid for example, promoters or introns or 31 untranslated region or 51untranslated regions of genes to increase expression or alterspecificity of expression of proteins. The approach may also be used tomutate ribozymes or aptamers.

Shuffling requires the presence of homologous regions separating regionsof diversity. Scaffold-like protein structures may be particularlysuitable for shuffling. The conserved scaffold determines the overallfolding by self-association, while displaying relatively unrestrictedloops that mediate the specific binding. Examples of such scaffolds arethe immunoglobulin beta-barrel, and the four-helix bundle which arewell-known in the art. This shuffling can be used to createscaffold-like proteins with various combinations of mutated sequencesfor binding.

Saturation Mutagenesis

In one aspect, this invention provides for the use of proprietary codonprimers (containing a degenerate N,N,G/T sequence) to introduce pointmutations into a polynucleotide, so as to generate a set of progenypolypeptides in which a full range of single amino acid substitutions isrepresented at each amino acid position. The oligos used are comprisedcontiguously of a first homologous sequence, a degenerate N,N,G/Tsequence, and preferably but not necessarily a second homologoussequence. The downstream progeny translational products from the use ofsuch oligos include all possible amino acid changes at each amino acidsite along the polypeptide, because the degeneracy of the N,N,G/Tsequence includes codons for all 20 amino acids.

In one aspect, one such degenerate oligo (comprised of one degenerateN,N,G/T cassette) is used for subjecting each original codon in aparental polynucleotide template to a full range of codon substitutions.In another aspect, at least two degenerate N,N,G/T cassettes areused—either in the same oligo or not, for subjecting at least twooriginal codons in a parental polynucleotide template to a full range ofcodon substitutions. Thus, more than one N,N,G/T sequence can becontained in one oligo to introduce amino acid mutations at more thanone site. This plurality of N,N,G/T sequences can be directlycontiguous, or separated by one or more additional nucleotidesequence(s). In another aspect, oligos serviceable for introducingadditions and deletions can be used either alone or in combination withthe codons containing an N,N,G/T sequence, to introduce any combinationor permutation of amino acid additions, deletions, and/or substitutions.

In a particular exemplification, it is possible to simultaneouslymutagenize two or more contiguous amino acid positions using an oligothat contains contiguous N,N,G/T triplets, i.e. a degenerate (N,N,G/T)nsequence.

In another aspect, the present invention provides for the use ofdegenerate cassettes having less degeneracy than the N,N,G/T sequence.For example, it may be desirable in some instances to use (e.g. in anoligo) a degenerate triplet sequence comprised of only one N, where saidN can be in the first second or third position of the triplet. Any otherbases including any combinations and permutations thereof can be used inthe remaining two positions of the triplet. Alternatively, it may bedesirable in some instances to use (e.g. in an oligo) a degenerate N,N,Ntriplet sequence, or an N,N, G/C triplet sequence.

It is appreciated, however, that the use of a degenerate triplet (suchas N,N,G/T or an N,N, G/C triplet sequence) as disclosed in the instantinvention is advantageous for several reasons. In one aspect, thisinvention provides a means to systematically and fairly easily generatethe substitution of the full range of possible amino acids (for a totalof 20 amino acids) into each and every amino acid position in apolypeptide. Thus, for a 100 amino acid polypeptide, the instantinvention provides a way to systematically and fairly easily generate2000 distinct species (i.e. 20 possible amino acids per position X 100amino acid positions). It is appreciated that there is provided, throughthe use of an oligo containing a degenerate N,N,G/T or an N,N, G/Ctriplet sequence, 32 individual sequences that code for 20 possibleamino acids. Thus, in a reaction vessel in which a parentalpolynucleotide sequence is subjected to saturation mutagenesis using onesuch oligo, there are generated 32 distinct progeny polynucleotidesencoding 20 distinct polypeptides. In contrast, the use of anon-degenerate oligo in site-directed mutagenesis leads to only oneprogeny polypeptide product per reaction vessel.

This invention also provides for the use of nondegenerate oligos, whichcan optionally be used in combination with degenerate primers disclosed.It is appreciated that in some situations, it is advantageous to usenondegenerate oligos to generate specific point mutations in a workingpolynucleotide. This provides a means to generate specific silent pointmutations, point mutations leading to corresponding amino acid changes,and point mutations that cause the generation of stop codons and thecorresponding expression of polypeptide fragments.

Thus, in a preferred embodiment of this invention, each saturationmutagenesis reaction vessel contains polynucleotides encoding at least20 progeny polypeptide molecules such that all 20 amino acids arerepresented at the one specific amino acid position corresponding to thecodon position mutagenized in the parental polynucleotide. The 32-folddegenerate progeny polypeptides generated from each saturationmutagenesis reaction vessel can be subjected to clonal amplification(e.g. cloned into a suitable E. coli host using an expression vector)and subjected to expression screening. When an individual progenypolypeptide is identified by screening to display a favorable change inproperty (when compared to the parental polypeptide), it can besequenced to identify the correspondingly favorable amino acidsubstitution contained therein.

It is appreciated that upon mutagenizing each and every amino acidposition in a parental polypeptide using saturation mutagenesis asdisclosed herein, favorable amino acid changes may be identified at morethan one amino acid position. One or more new progeny molecules can begenerated that contain a combination of all or part of these favorableamino acid substitutions. For example, if 2 specific favorable aminoacid changes are identified in each of 3 amino acid positions in apolypeptide, the permutations include 3 possibilities at each position(no change from the original amino acid, and each of two favorablechanges) and 3 positions. Thus, there are 3×3×3 or 27 totalpossibilities, including 7 that were previously examined—6 single pointmutations (i.e. 2 at each of three positions) and no change at anyposition.

In yet another aspect, site-saturation mutagenesis can be used togetherwith shuffling, chimerization, recombination and other mutagenizingprocesses, along with screening. This invention provides for the use ofany mutagenizing process(es), including saturation mutagenesis, in aniterative manner. In one exemplification, the iterative use of anymutagenizing process(es) is used in combination with screening.

Thus, in a non-limiting exemplification, this invention provides for theuse of saturation mutagenesis in combination with additionalmutagenization processes, such as process where two or more relatedpolynucleotides are introduced into a suitable host cell such that ahybrid polynucleotide is generated by recombination and reductivereassortment.

In addition to performing mutagenesis along the entire sequence of agene, the instant invention provides that mutagenesis can be use toreplace each of any number of bases in a polynucleotide sequence,wherein the number of bases to be mutagenized is preferably everyinteger from 15 to 100,000. Thus, instead of mutagenizing every positionalong a molecule, one can subject every a discrete number of bases(preferably a subset totaling from 15 to 100,000) to mutagenesis.Preferably, a separate nucleotide is used for mutagenizing each positionor group of positions along a polynucleotide sequence. A group of 3positions to be mutagenized may be a codon. The mutations are preferablyintroduced using a mutagenic primer, containing a heterologous cassette,also referred to as a mutagenic cassette. Preferred cassettes can havefrom 1 to 500 bases. Each nucleotide position in such heterologouscassettes be N, A, C, G, T, A/C, A/G, A/T, C/G, C/T, G/T, C/G/T, A/G/T,A/C/T, A/C/G, or E, where E is any base that is not A, C, G, or T (E canbe referred to as a designer oligo). The tables below show exemplarytri-nucleotide cassettes (there are over 3000 possibilities in additionto N,N,G/T and N,N,N and N,N,A/C).

In a general sense, saturation mutagenesis is comprised of mutagenizinga complete set of mutagenic cassettes (wherein each cassette ispreferably 1-500 bases in length) in defined polynucleotide sequence tobe mutagenized (wherein the sequence to be mutagenized is preferablyfrom 15 to 100,000 bases in length). Thusly, a group of mutations(ranging from 1 to 100 mutations) is introduced into each cassette to bemutagenized. A grouping of mutations to be introduced into one cassettecan be different or the same from a second grouping of mutations to beintroduced into a second cassette during the application of one round ofsaturation mutagenesis. Such groupings are exemplified by deletions,additions, groupings of particular codons, and groupings of particularnucleotide cassettes.

Defined sequences to be mutagenized (see FIG. 20) include preferably awhole gene, pathway, cDNA, an entire open reading frame (ORF), andintire promoter, enhancer, repressor/transactivator, origin ofreplication, intron, operator, or any polynucleotide functional group.Generally, a preferred “defined sequences” for this purpose may be anypolynucleotide that a 15 base-polynucleotide sequence, andpolynucleotide sequences of lengths between 15 bases and 15,000 bases(this invention specifically names every integer in between).Considerations in choosing groupings of codons include types of aminoacids encoded by a degenerate mutagenic cassette.

In a particularly preferred exemplification a grouping of mutations thatcan be introduced into a mutagenic cassette, this invention specificallyprovides for degenerate codon substitutions (using degenerate oligos)that code for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, and 20 amino acids at each position, and a library ofpolypeptides encoded thereby.

Chimerizations

In Vitro Shuffling

The equivalents of some standard genetic matings may also be performedby shuffling in vitro. For example, a “molecular backcross” can beperformed by repeatedly mixing the hybrid's nucleic acid with thewild-type nucleic acid while selecting for the mutations of interest. Asin traditional breeding, this approach can be used to combine phenotypesfrom different sources into a background of choice. It is useful, forexample, for the removal of neutral mutations that affect unselectedcharacteristics (i.e. immunogenicity). Thus it can be useful todetermine which mutations in a protein are involved in the enhancedbiological activity and which are not, an advantage which cannot beachieved by error-prone mutagenesis or cassette mutagenesis methods.

Large, functional genes can be assembled correctly from a mixture ofsmall random polynucleotides. This reaction may be of use for thereassembly of genes from the highly fragmented DNA of fossils. Inaddition random nucleic acid fragments from fossils may be combined withpolynucleotides from similar genes from related species.

It is also contemplated that the method of this invention can be usedfor the in vitro amplification of a whole genome from a single cell asis needed for a variety of research and diagnostic applications. DNAamplification by PCR is in practice limited to a length of about 40 kb.Amplification of a whole genome such as that of E. coli (5,000 kb) byPCR would require about 250 primers yielding 125 forty kbpolynucleotides. This approach is not practical due to theunavailability of sufficient sequence data. On the other hand, randomproduction of polynucleotides of the genome with sexual PCR cycles,followed by gel purification of small polynucleotides will provide amultitude of possible primers. Use of this mix of random smallpolynucleotides as primers in a PCR reaction alone or with the wholegenome as the template should result in an inverse chain reaction withthe theoretical endpoint of a single concatamer containing many copiesof the genome.

100 fold amplification in the copy number and an average polynucleotidesize of greater than 50 kb may be obtained when only randompolynucleotides are used. It is thought that the larger concatamer isgenerated by overlap of many smaller polynucleotides. The quality ofspecific PCR products obtained using synthetic primers will beindistinguishable from the product obtained from unamplified DNA. It isexpected that this approach will be useful for the mapping of genomes.

The polynucleotide to be shuffled can be produced as random ornon-random polynucleotides, at the discretion of the practitioner.Moreover, this invention provides a method of shuffling that isapplicable to a wide range of polynucleotide sizes and types, includingthe step of generating polynucleotide monomers to be used as buildingblocks in the reassembly of a larger polynucleotide. For example, thebuilding blocks can be fragments of genes or they can be comprised ofentire genes or gene pathways, or any combination thereof.

Exonuclease-Mediated Shuffling

In a particular embodiment, this invention provides for a method forshuffling, assembling, reassembling, recombining, &/or concatenating atleast two polynucleotides to form a progeny polynucleotide (e.g. achimeric progeny polynucleotide that can be expressed to produce apolypeptide or a gene pathway). In a particular embodiment, a doublestranded polynucleotide end (e.g. two single stranded sequenceshybridized to each other as hybridization partners) is treated with anexonuclease to liberate nucleotides from one of the two strands, leavingthe remaining strand free of its original partner so that, if desired,the remaining strand may be used to achieve hybridization to anotherpartner.

In a particular aspect, a double stranded polynucleotide end (that maybe part of—or connected to—a polynucleotide or a nonpolynucleotidesequence) is subjected to a source of exonuclease activity. Serviceablesources of exonuclease activity may be an enzyme with 3′ exonucleaseactivity, an enzyme with 5′ exonuclease activity, an enzyme with both 3′exonuclease activity and 5′ exonuclease activity, and any combinationthereof. An exonuclease can be used to liberate nucleotides from one orboth ends of a linear double stranded polynucleotide, and from one toall ends of a branched polynucleotide having more than two ends. Themechanism of action of this liberation is believed to be comprised of anenzymatically-catalyzed hydrolysis of terminal nucleotides, and can beallowed to proceed in a time-dependent fashion, allowing experimentalcontrol of the progression of the enzymatic process.

By contrast, a non-enzymatic step may be used to shuffle, assemble,reassemble, recombine, and/or concatenate polynucleotide building blocksthat is comprised of subjecting a working sample to denaturing (or“melting”) conditions (for example, by changing temperature, pH, and/orsalinity conditions) so as to melt a working set of double strandedpolynucleotides into single polynucleotide strands. For shuffling, it isdesirable that the single polynucleotide strands participate to someextent in annealment with different hybridization partners (i.e. and notmerely revert to exclusive reannealment between what were formerpartners before the denaturation step). The presence of the formerhybridization partners in the reaction vessel, however, does notpreclude, and may sometimes even favor, reannealment of a singlestranded polynucleotide with its former partner, to recreate an originaldouble stranded polynucleotide.

In contrast to this non-enzymatic shuffling step comprised of subjectingdouble stranded polynucleotide building blocks to denaturation, followedby annealment, the instant invention further provides anexonuclease-based approach requiring no denaturation—rather, theavoidance of denaturing conditions and the maintenance of doublestranded polynucleotide substrates in annealed (i.e. non-denatured)state are necessary conditions for the action of exonucleases (e.g.,exonuclease III and red alpha gene product). Additionally in contrast,the generation of single stranded polynucleotide sequences capable ofhybridizing to other single stranded polynucleotide sequences is theresult of covalent cleavage—and hence sequence destruction—in one of thehybridization partners. For example, an exonuclease III enzyme may beused to enzymatically liberate 3′ terminal nucleotides in onehybridization strand (to achieve covalent hydrolysis in thatpolynucleotide strand); and this favors hybridization of the remainingsingle strand to a new partner (since its former partner was subjectedto covalent cleavage).

By way of further illustration, a specific exonuclease, namelyexonuclease III is provided herein as an example of a 3′ exonuclease;however, other exonucleases may also be used, including enzymes with 5′exonuclease activity and enzymes with 3′ exonuclease activity, andincluding enzymes not yet discovered and enzymes not yet developed. Itis particularly appreciated that enzymes can be discovered, optimized(e.g. engineered by directed evolution), or both discovered andoptimized specifically for the instantly disclosed approach that havemore optimal rates &/or more highly specific activities &/or greaterlack of unwanted activities. In fact it is expected that the instantinvention may encourage the discovery &/or development of such designerenzymes. In sum, this invention may be practiced with a variety ofcurrently available exonuclease enzymes, as well enzymes not yetdiscovered and enzymes not yet developed.

The exonuclease action of exonuclease III requires a working doublestranded polynucleotide end that is either blunt or has a 5′ overhang,and the exonuclease action is comprised of enzymatically liberating 3′terminal nucleotides, leaving a single stranded 5′ end that becomeslonger and longer as the exonuclease action proceeds (see FIG. 1). Any5′ overhangs produced by this approach may be used to hybridize toanother single stranded polynucleotide sequence (which may also be asingle stranded polynucleotide or a terminal overhang of a partiallydouble stranded polynucleotide) that shares enough homology to allowhybridization. The ability of these exonuclease III-generated singlestranded sequences (e.g. in 5′ overhangs) to hybridize to other singlestranded sequences allows two or more polynucleotides to be shuffled,assembled, reassembled, &/or concatenated.

Furthermore, it is appreciated that one can protect the end of a doublestranded polynucleotide or render it susceptible to a desired enzymaticaction of a serviceable exonuclease as necessary. For example, a doublestranded polynucleotide end having a 3′ overhang is not susceptible tothe exonuclease action of exonuclease III. However, it may be renderedsusceptible to the exonuclease action of exonuclease III by a variety ofmeans; for example, it may be blunted by treatment with a polymerase,cleaved to provide a blunt end or a 5′ overhang, joined (ligated orhybridized) to another double stranded polynucleotide to provide a bluntend or a 5′ overhang, hybridized to a single stranded polynucleotide toprovide a blunt end or a 5′ overhang, or modified by any of a variety ofmeans).

According to one aspect, an exonuclease may be allowed to act on one oron both ends of a linear double stranded polynucleotide and proceed tocompletion, to near completion, or to partial completion. When theexonuclease action is allowed to go to completion, the result will bethat the length of each 5′ overhang will be extend far towards themiddle region of the polynucleotide in the direction of what might beconsidered a “rendezvous point” (which may be somewhere near thepolynucleotide midpoint). Ultimately, this results in the production ofsingle stranded polynucleotides (that can become dissociated) that areeach about half the length of the original double strandedpolynucleotide (see FIG. 1). Alternatively, an exonuclease-mediatedreaction can be terminated before proceeding to completion.

Thus this exonuclease-mediated approach is serviceable for shuffling,assembling &/or reassembling, recombining, and concatenatingpolynucleotide building blocks, which polynucleotide building blocks canbe up to ten bases long or tens of bases long or hundreds of bases longor thousands of bases long or tens of thousands of bases long orhundreds of thousands of bases long or millions of bases long or evenlonger.

This exonuclease-mediated approach is based on the action of doublestranded DNA specific exodeoxyribonuclease activity of E. coliexonuclease III. Substrates for exonuclease III may be generated bysubjecting a double stranded polynucleotide to fragmentation.Fragmentation may be achieved by mechanical means (e.g., shearing,sonication, etc.), by enzymatic means (e.g. using restriction enzymes),and by any combination thereof. Fragments of a larger polynucleotide mayalso be generated by polymerase-mediated synthesis.

Exonuclease III is a 28K monomeric enzyme, product of the xthA gene ofE. coli with four known activities: exodeoxyribonuclease (alternativelyreferred to as exonuclease herein), RNaseH, DNA-3′-phosphatase, and APendonuclease. The exodeoxyribonuclease activity is specific for doublestranded DNA. The mechanism of action is thought to involve enzymatichydrolysis of DNA from a 3′ end progressively towards a 5′ direction,with formation of nucleoside 5′-phosphates and a residual single strand.The enzyme does not display efficient hydrolysis of single stranded DNA,single-stranded RNA, or double-stranded RNA; however it degrades RNA inan DNA-RNA hybrid releasing nucleoside 5′-phosphates. The enzyme alsoreleases inorganic phosphate specifically from 3′phosphomonoester groupson DNA, but not from RNA or short oligonucleotides. Removal of thesegroups converts the terminus into a primer for DNA polymerase action.

Additional examples of enzymes with exonuclease activity includered-alpha and venom phosphodiesterases. Red alpha (red a) gene product(also referred to as lambda exonuclease) is of bacteriophage λ, origin.The redα gene is transcribed from the leftward promoter and its productis involved (24 kD) in recombination. Red alpha gene product actsprocessively from 5′-phosphorylated termini to liberate mononucleotidesfrom duplex DNA (Takahashi & Kobayashi, 1990). Venom phosphodiesterases(Laskowski, 1980) is capable of rapidly opening supercoiled DNA.

Synthetic Ligation Reassembly

In one aspect, the present invention provides a non-stochastic methodtermed synthetic ligation reassembly (SLR), that is somewhat related tostochastic shuffling, save that the nucleic acid building blocks are notshuffled or concatenated or chimerized randomly, but rather areassembled non-stochastically.

A particularly glaring difference is that the instant SLR method doesnot depend on the presence of a high level of homology betweenpolynucleotides to be shuffled. In contrast, prior methods, particularlyprior stochastic shuffling methods require that presence of a high levelof homology, particularly at coupling sites, between polynucleotides tobe shuffled. Accordingly these prior methods favor the regeneration ofthe original progenitor molecules, and are suboptimal for generatinglarge numbers of novel progeny chimeras, particularly full-lengthprogenies. The instant invention, on the other hand, can be used tonon-stochastically generate libraries (or sets) of progeny moleculescomprised of over 10¹⁰⁰ different chimeras. Conceivably, SLR can even beused to generate libraries comprised of over 10¹⁰⁰⁰ different progenychimeras with (no upper limit in sight).

Thus, in one aspect, the present invention provides a method, whichmethod is non-stochastic, of producing a set of finalized chimericnucleic acid molecules having an overall assembly order that is chosenby design, which method is comprised of the steps of generating bydesign a plurality of specific nucleic acid building blocks havingserviceable mutually compatible ligatable ends, and assembling thesenucleic acid building blocks, such that a designed overall assemblyorder is achieved.

The mutually compatible ligatable ends of the nucleic acid buildingblocks to be assembled are considered to be “serviceable” for this typeof ordered assembly if they enable the building blocks to be coupled inpredetermined orders. Thus, in one aspect, the overall assembly order inwhich the nucleic acid building blocks can be coupled is specified bythe design of the ligatable ends and, if more than one assembly step isto be used, then the overall assembly order in which the nucleic acidbuilding blocks can be coupled is also specified by the sequential orderof the assembly step(s). FIG. 4, Panel C illustrates an exemplaryassembly process comprised of 2 sequential steps to achieve a designed(non-stochastic) overall assembly order for five nucleic acid buildingblocks. In a preferred embodiment of this invention, the annealedbuilding pieces are treated with an enzyme, such as a ligase (e.g. T4DNA ligase), achieve covalent bonding of the building pieces.

In a preferred embodiment, the design of nucleic acid building blocks isobtained upon analysis of the sequences of a set of progenitor nucleicacid templates that serve as a basis for producing a progeny set offinalized chimeric nucleic acid molecules. These progenitor nucleic acidtemplates thus serve as a source of sequence information that aids inthe design of the nucleic acid building blocks that are to bemutagenized, i.e. chimerized or shuffled.

In one exemplification, this invention provides for the chimerization ofa family of related genes and their encoded family of related products.In a particular exemplification, the encoded products are enzymes. As arepresentative list of families of enzymes which may be mutagenized inaccordance with the aspects of the present invention, there may bementioned, the following enzymes and their functions:

1 Lipase/Esterase

-   -   a. Enantioselective hydrolysis of esters (lipids)/thioesters        -   1) Resolution of racemic mixtures        -   2) Synthesis of optically active acids or alcohols from            meso-diesters    -   b. Selective syntheses        -   1) Regiospecific hydrolysis of carbohydrate esters        -   2) Selective hydrolysis of cyclic secondary alcohols    -   c. Synthesis of optically active esters, lactones, acids,        alcohols        -   1) Transesterification of activated/nonactivated esters        -   2) Interesterification        -   3) Optically active lactones from hydroxyesters        -   4) Regio- and enantioselective ring opening of anhydrides    -   d. Detergents    -   e. Fat/Oil conversion    -   f. Cheese ripening

2 Protease

-   -   a. Ester/amide synthesis    -   b. Peptide synthesis    -   c. Resolution of racemic mixtures of amino acid esters    -   d. Synthesis of non-natural amino acids    -   e. Detergents/protein hydrolysis

3 Glycosidase/Glycosyl transferase

-   -   a. Sugar/polymer synthesis    -   b. Cleavage of glycosidic linkages to form mono, di- and        oligosaccharides    -   c. Synthesis of complex oligosaccharides    -   d. Glycoside synthesis using UDP-galactosyl transferase    -   e. Transglycosylation of disaccharides, glycosyl fluorides, aryl        galactosides    -   f. Glycosyl transfer in oligosaccharide synthesis    -   g. Diastereoselective cleavage of β-glucosylsulfoxides    -   h. Asymmetric glycosylations    -   i. Food processing    -   j. Paper processing

4 Phosphatase/Kinase

-   -   a. Synthesis/hydrolysis of phosphate esters        -   1) Regio-, enantioselective phosphorylation        -   2) Introduction of phosphate esters        -   3) Synthesize phospholipid precursors        -   4) Controlled polynucleotide synthesis    -   b. Activate biological molecule    -   c. Selective phosphate bond formation without protecting groups

5 Mono/Dioxygenase

-   -   a. Direct oxyfunctionalization of unactivated organic substrates    -   b. Hydroxylation of alkane, aromatics, steroids    -   c. Epoxidation of alkenes    -   d. Enantioselective sulphoxidation    -   e. Regio- and stereoselective Bayer-Villiger oxidations

6 Haloperoxidase

-   -   a. Oxidative addition of halide ion to nucleophilic sites    -   b. Addition of hypohalous acids to olefinic bonds    -   c. Ring cleavage of cyclopropanes    -   d. Activated aromatic substrates converted to ortho and para        derivatives    -   e. 1.3 diketones converted to 2-halo-derivatives    -   f. Heteroatom oxidation of sulfur and nitrogen containing        substrates    -   g. Oxidation of enol acetates, alkynes and activated aromatic        rings

7 Lignin peroxidase/Diarylpropane peroxidase

-   -   a. Oxidative cleavage of C—C bonds    -   b. Oxidation of benzylic alcohols to aldehydes    -   c. Hydroxylation of benzylic carbons    -   d. Phenol dimerization    -   e. Hydroxylation of double bonds to form diols    -   f. Cleavage of lignin aldehydes

8 Epoxide hydrolase

-   -   a. Synthesis of enantiomerically pure bioactive compounds    -   b. Regio- and enantioselective hydrolysis of epoxide    -   c. Aromatic and olefinic epoxidation by monooxygenases to form        epoxides    -   d. Resolution of racemic epoxides    -   e. Hydrolysis of steroid epoxides

9 Nitrile hydratase/nitrilase

-   -   a. Hydrolysis of aliphatic nitriles to carboxamides    -   b. Hydrolysis of aromatic, heterocyclic, unsaturated aliphatic        nitriles to corresponding acids    -   c. Hydrolysis of acrylonitrile    -   d. Production of aromatic and carboxamides, carboxylic acids        (nicotinamide, picolinamide, isonicotinamide)    -   e. Regioselective hydrolysis of acrylic dinitrile    -   f. α-amino acids from α-hydroxynitriles

10 Transaminase

-   -   a. Transfer of amino groups into oxo-acids

11 Amidase/Acylase

-   -   a. Hydrolysis of amides, amidines, and other C—N bonds    -   b. Non-natural amino acid resolution and synthesis

These exemplifications, while illustrating certain specific aspects ofthe invention, do not portray the limitations or circumscribe the scopeof the disclosed invention.

Thus according to one aspect of this invention, the sequences of aplurality of progenitor nucleic acid templates are aligned in order toselect one or more demarcation points, which demarcation points can belocated at an area of homology, and are comprised of one or morenucleotides, and which demarcation points are shared by at least two ofthe progenitor templates. The demarcation points can be used todelineate the boundaries of nucleic acid building blocks to begenerated. Thus, the demarcation points identified and selected in theprogenitor molecules serve as potential chimerization points in theassembly of the progeny molecules.

Preferably a serviceable demarcation point is an area of homology(comprised of at least one homologous nucleotide base) shared by atleast two progenitor templates. More preferably a serviceabledemarcation point is an area of homology that is shared by at least halfof the progenitor templates. More preferably still a serviceabledemarcation point is an area of homology that is shared by at least twothirds of the progenitor templates. Even more preferably a serviceabledemarcation points is an area of homology that is shared by at leastthree fourths of the progenitor templates. Even more preferably still aserviceable demarcation points is an area of homology that is shared byat almost all of the progenitor templates. Even more preferably still aserviceable demarcation point is an area of homology that is shared byall of the progenitor templates.

The process of designing nucleic acid building blocks and of designingthe mutually compatible ligatable ends of the nucleic acid buildingblocks to be assembled is illustrated in FIGS. 6 and 7. As shown, thealignment of a set of progenitor templates reveals several naturallyoccurring demarcation points, and the identification of demarcationpoints shared by these templates helps to non-stochastically determinethe building blocks to be generated and used for the generation of theprogeny chimeric molecules.

In a preferred embodiment, this invention provides that the ligationreassembly process is performed exhaustively in order to generate anexhaustive library. In other words, all possible ordered combinations ofthe nucleic acid building blocks are represented in the set of finalizedchimeric nucleic acid molecules. At the same time, in a particularlypreferred embodiment, the assembly order (i.e. the order of assembly ofeach building block in the 5′ to 3 sequence of each finalized chimericnucleic acid) in each combination is by design (or non-stochastic).Because of the non-stochastic nature of this invention, the possibilityof unwanted side products is greatly reduced.

In another preferred embodiment, this invention provides that, theligation reassembly process is performed systematically, for example inorder to generate a systematically compartmentalized library, withcompartments that can be screened systematically, e.g. one by one. Inother words this invention provides that, through the selective andjudicious use of specific nucleic acid building blocks, coupled with theselective and judicious use of sequentially stepped assembly reactions,an experimental design can be achieved where specific sets of progenyproducts are made in each of several reaction vessels. This allows asystematic examination and screening procedure to be performed. Thus, itallows a potentially very large number of progeny molecules to beexamined systematically in smaller groups.

Because of its ability to perform chimerizations in a manner that ishighly flexible yet exhaustive and systematic as well, particularly whenthere is a low level of homology among the progenitor molecules, theinstant invention provides for the generation of a library (or set)comprised of a large number of progeny molecules. Because of thenon-stochastic nature of the instant ligation reassembly invention, theprogeny molecules generated preferably comprise a library of finalizedchimeric nucleic acid molecules having an overall assembly order that ischosen by design. In a particularly preferred embodiment of thisinvention, such a generated library is comprised of preferably greaterthan 10³ different progeny molecular species, more preferably greaterthan 10⁵ different progeny molecular species, more preferably stillgreater than 10¹⁰ different progeny molecular species, more preferablystill greater than 10¹⁵ different progeny molecular species, morepreferably still greater than 10²⁰ different progeny molecular species,more preferably still greater than 10³⁰ different progeny molecularspecies, more preferably still greater than 10⁴⁰ different progenymolecular species, more preferably still greater than 10⁵⁰ differentprogeny molecular species, more preferably still greater than 10⁶⁰different progeny molecular species, more preferably still greater than10⁷⁰ different progeny molecular species, more preferably still greaterthan 10⁸⁰ different progeny molecular species, more preferably stillgreater than 10¹⁰⁰ different progeny molecular species, more preferablystill greater than 10¹¹⁰ different progeny molecular species, morepreferably still greater than 10¹²⁰ different progeny molecular species,more preferably still greater than 10¹³⁰ different progeny molecularspecies, more preferably still greater than 10¹⁴⁰ different progenymolecular species, more preferably still greater than 10¹⁵⁰ differentprogeny molecular species, more preferably still greater than 10¹⁷⁵different progeny molecular species, more preferably still greater than10²⁰⁰ different progeny molecular species, more preferably still greaterthan 10³⁰⁰ different progeny molecular species, more preferably stillgreater than 10⁴⁰⁰ different progeny molecular species, more preferablystill greater than 10⁵⁰⁰ different progeny molecular species, and evenmore preferably still greater than 10¹⁰⁰⁰ different progeny molecularspecies.

In one aspect, a set of finalized chimeric nucleic acid molecules,produced as described is comprised of a polynucleotide encoding apolypeptide. According to one preferred embodiment, this polynucleotideis a gene, which may be a man-made gene. According to another preferredembodiment, this polynucleotide is a gene pathway, which may be aman-made gene pathway. This invention provides that one or more man-madegenes generated by this invention may be incorporated into a man-madegene pathway, such as pathway operable in a eukaryotic organism(including a plant).

It is appreciated that the power of this invention is exceptional, asthere is much freedom of choice and control regarding the selection ofdemarcation points, the size and number of the nucleic acid buildingblocks, and the size and design of the couplings. It is appreciated,furthermore, that the requirement for intermolecular homology is highlyrelaxed for the operability of this invention. In fact, demarcationpoints can even be chosen in areas of little or no intermolecularhomology. For example, because of codon wobble, i.e. the degeneracy ofcodons, nucleotide substitutions can be introduced into nucleic acidbuilding blocks without altering the amino acid originally encoded inthe corresponding progenitor template. Alternatively, a codon can bealtered such that the coding for an originally amino acid is altered.This invention provides that such substitutions can be introduced intothe nucleic acid building block in order to increase the incidence ofintermolecularly homologous demarcation points and thus to allow anincreased number of couplings to be achieved among the building blocks,which in turn allows a greater number of progeny chimeric molecules tobe generated.

In another exemplification, the synthetic nature of the step in whichthe building blocks are generated allows the design and introduction ofnucleotides (e.g. one or more nucleotides, which may be, for example,codons or introns or regulatory sequences) that can later be optionallyremoved in an in vitro process (e.g. by mutagenesis) or in an in vivoprocess (e.g. by utilizing the gene splicing ability of a hostorganism). It is appreciated that in many instances the introduction ofthese nucleotides may also be desirable for many other reasons inaddition to the potential benefit of creating a serviceable demarcationpoint.

Thus, according to another embodiment, this invention provides that anucleic acid building block can be used to introduce an intron. Thus,this invention provides that functional introns may be introduced into aman-made gene of this invention. This invention also provides thatfunctional introns may be introduced into a man-made gene pathway ofthis invention. Accordingly, this invention provides for the generationof a chimeric polynucleotide that is a man-made gene containing one (ormore) artificially introduced intron(s).

Accordingly, this invention also provides for the generation of achimeric polynucleotide that is a man-made gene pathway containing one(or more) artificially introduced intron(s). Preferably, theartificially introduced intron(s) are functional in one or more hostcells for gene splicing much in the way that naturally-occurring intronsserve functionally in gene splicing. This invention provides a processof producing man-made intron-containing polynucleotides to be introducedinto host organisms for recombination and/or splicing.

The ability to achieve chimerizations, using couplings as describedherein, in areas of little or no homology among the progenitormolecules, is particularly useful, and in fact critical, for theassembly of novel gene pathways. This invention thus provides for thegeneration of novel man-made gene pathways using synthetic ligationreassembly. In a particular aspect, this is achieved by the introductionof regulatory sequences, such as promoters, that are operable in anintended host, to confer operability to a novel gene pathway when it isintroduced into the intended host. In a particular exemplification, thisinvention provides for the generation of novel man-made gene pathwaysthat is operable in a plurality of intended hosts (e.g. in a microbialorganism as well as in a plant cell). This can be achieve, for example,by the introduction of a plurality of regulatory sequences, comprised ofa regulatory sequence that is operable in a first intended host and aregulatory sequence that is operable in a second intended host. Asimilar process can be performed to achieve operability of a genepathway in a third intended host species, etc. The number of intendedhost species can be each integer from 1 to 10 or alternatively over 10.Alternatively, for example, operability of a gene pathway in a pluralityof intended hosts can be achieved by the introduction of a regulatorysequence having intrinsic operability in a plurality of intended hosts.

Thus, according to a particular embodiment, this invention provides thata nucleic acid building block can be used to introduce a regulatorysequence, particularly a regulatory sequence for gene expression.Preferred regulatory sequences include, but are not limited to, thosethat are man-made, and those found in archeal, bacterial, eukaryotic(including mitochondrial), viral, and prionic or prion-like organisms.Preferred regulatory sequences include but are not limited to,promoters, operators, and activator binding sites. Thus, this inventionprovides that functional regulatory sequences may be introduced into aman-made gene of this invention. This invention also provides thatfunctional regulatory sequences may be introduced into a man-made genepathway of this invention.

Accordingly, this invention provides for the generation of a chimericpolynucleotide that is a man-made gene containing one (or more)artificially introduced regulatory sequence(s). Accordingly, thisinvention also provides for the generation of a chimeric polynucleotidethat is a man-made gene pathway containing one (or more) artificiallyintroduced regulatory sequence(s). Preferably, an artificiallyintroduced regulatory sequence(s) is operatively linked to one or moregenes in the man-made polynucleotide, and are functional in one or morehost cells.

Preferred bacterial promoters that are serviceable for this inventioninclude lacI, lacZ, T3, T7, gpt, lambda P_(R), P_(L) and trp.Serviceable eukaryotic promoters include CMV immediate early, HSVthymidine kinase, early and late SV40, LTRs from retrovirus, and mousemetallothionein-I. Particular plant regulatory sequences includepromoters active in directing transcription in plants, eitherconstitutively or stage and/or tissue specific, depending on the use ofthe plant or parts thereof. These promoters include, but are not limitedto promoters showing constitutive expression, such as the 35S promoterof Cauliflower Mosaic Virus (CaMV) (Guilley et al., 1982), those forleaf-specific expression, such as the promoter of the ribulosebisphosphate carboxylase small subunit gene (Coruzzi et al., 1984),those for root-specific expression, such as the promoter from theglutamin synthase gene (Tingey et al., 1987), those for seed-specificexpression, such as the cruciferin A promoter from Brassica napus (Ryanet al., 1989), those for tuber-specific expression, such as the class-Ipatatin promoter from potato (Rocha-Sasa et al., 1989; Wenzler et al.,1989) or those for fruit-specific expression, such as thepolygalacturonase (PG) promoter from tomato (Bird et al., 1988).

Other regulatory sequences that are preferred for this invention includeterminator sequences and polyadenylation signals and any such sequencefunctioning as such in plants, the choice of which is within the levelof the skilled artisan. An example of such sequences is the 3′ flankingregion of the nopaline synthase (nos) gene of Agrobacterium tumefaciens(Bevan, 1984). The regulatory sequences may also include enhancersequences, such as found in the 35S promoter of CaMV, and mRNAstabilizing sequences such as the leader sequence of Alfalfa MosaicCirus (A1MV) RNA4 (Brederode et al., 1980) or any other sequencesfunctioning in a like manner.

A man-made genes produced using this invention can also serve as asubstrate for recombination with another nucleic acid. Likewise, aman-made gene pathway produced using this invention can also serve as asubstrate for recombination with another nucleic acid. In a preferredinstance, the recombination is facilitated by, or occurs at, areas ofhomology between the man-made intron-containing gene and a nucleic acidwith serves as a recombination partner. In a particularly preferredinstance, the recombination partner may also be a nucleic acid generatedby this invention, including a man-made gene or a man-made gene pathway.Recombination may be facilitated by or may occur at areas of homologythat exist at the one (or more) artificially introduced intron(s) in theman-made gene.

The synthetic ligation reassembly method of this invention utilizes aplurality of nucleic acid building blocks, each of which preferably hastwo ligatable ends. The two ligatable ends on each nucleic acid buildingblock may be two blunt ends (i.e. each having an overhang of zeronucleotides), or preferably one blunt end and one overhang, or morepreferably still two overhangs.

A serviceable overhang for this purpose may be a 3′ overhang or a 5′overhang. Thus, a nucleic acid building block may have a 3′ overhang oralternatively a 5′ overhang or alternatively two 3′ overhangs oralternatively two 5′ overhangs. The overall order in which the nucleicacid building blocks are assembled to form a finalized chimeric nucleicacid molecule is determined by purposeful experimental design and is notrandom.

According to one preferred embodiment, a nucleic acid building block isgenerated by chemical synthesis of two single-stranded nucleic acids(also referred to as single-stranded oligos) and contacting them so asto allow them to anneal to form a double-stranded nucleic acid buildingblock.

A double-stranded nucleic acid building block can be of variable size.The sizes of these building blocks can be small or large depending onthe choice of the experimenter. Preferred sizes for building block rangefrom 1 base pair (not including any overhangs) to 100,000 base pairs(not including any overhangs). Other preferred size ranges are alsoprovided, which have lower limits of from 1 bp to 10,000 bp (includingevery integer value in between), and upper limits of from 2 bp to100,000 bp (including every integer value in between).

It is appreciated that current methods of polymerase-based amplificationcan be used to generate double-stranded nucleic acids of up to thousandsof base pairs, if not tens of thousands of base pairs, in length withhigh fidelity. Chemical synthesis (e.g. phosphoramidite-based) can beused to generate nucleic acids of up to hundreds of nucleotides inlength with high fidelity; however, these can be assembled, e.g. usingoverhangs or sticky ends, to form double-stranded nucleic acids of up tothousands of base pairs, if not tens of thousands of base pairs, inlength if so desired.

A combination of methods (e.g. phosphoramidite-based chemical synthesisand PCR) can also be used according to this invention. Thus, nucleicacid building block made by different methods can also be used incombination to generate a progeny molecule of this invention.

The use of chemical synthesis to generate nucleic acid building blocksis particularly preferred in this invention & is advantageous for otherreasons as well, including procedural safety and ease. No cloning orharvesting or actual handling of any biological samples is required. Thedesign of the nucleic acid building blocks can be accomplished on paper.Accordingly, this invention teaches an advance in procedural safety inrecombinant technologies.

Nonetheless, according to one preferred embodiment, a double-strandednucleic acid building block according to this invention may also begenerated by polymerase-based amplification of a polynucleotidetemplate. In a non-limiting exemplification, as illustrated in FIG. 2, afirst polymerase-based amplification reaction using a first set ofprimers, F₂ and R₁, is used to generate a blunt-ended product (labeledReaction 1, Product 1), which is essentially identical to Product A. Asecond polymerase-based amplification reaction using a second set ofprimers, F₁ and R₂, is used to generate a blunt-ended product (labeledReaction 2, Product 2), which is essentially identical to Product B.These two products are mixed and allowed to melt and anneal, generatingpotentially useful double-stranded nucleic acid building blocks with twooverhangs. In the example of FIG. 2, the product with the 3′ overhangs(Product C) is selected by nuclease-based degradation of the other 3products using a 3′ acting exonuclease, such as exonuclease III. It isappreciated that a 5′ acting exonuclease (e.g. red alpha) may be also beused, for example to select Product D instead. It is also appreciatedthat other selection means can also be used, includinghybridization-based means, and that these means can incorporate afurther means, such as a magnetic bead-based means, to facilitateseparation of the desired product.

Many other methods exist by which a double-stranded nucleic acidbuilding block can be generated that is serviceable for this invention;and these are known in the art and can be readily performed by theskilled artisan.

According to particularly preferred embodiment, a double-strandednucleic acid building block that is serviceable for this invention isgenerated by first generating two single stranded nucleic acids andallowing them to anneal to form a double-stranded nucleic acid buildingblock. The two strands of a double-stranded nucleic acid building blockmay be complementary at every nucleotide apart from any that form anoverhang; thus containing no mismatches, apart from any overhang(s).According to another embodiment, the two strands of a double-strandednucleic acid building block are complementary at fewer than everynucleotide apart from any that form an overhang. Thus, according to thisembodiment, a double-stranded nucleic acid building block can be used tointroduce codon degeneracy. Preferably the codon degeneracy isintroduced using the site-saturation mutagenesis described herein, usingone or more N,N,G/T cassettes or alternatively using one or more N,N,Ncassettes.

Contained within an exemplary experimental design for achieving anordered assembly according to this invention are:

1) The design of specific nucleic acid building blocks.2) The design of specific ligatable ends on each nucleic acid buildingblock.3) The design of a particular order of assembly of the nucleic acidbuilding blocks.

An overhang may be a 3′ overhang or a 5′ overhang. An overhang may alsohave a terminal phosphate group or alternatively may be devoid of aterminal phosphate group (having, e.g., a hydroxyl group instead). Anoverhang may be comprised of any number of nucleotides. Preferably anoverhang is comprised of 0 nucleotides (as in a blunt end) to 10,000nucleotides. Thus, a wide range of overhang sizes may be serviceable.Accordingly, the lower limit may be each integer from 1-200 and theupper limit may be each integer from 2-10,000. According to a particularexemplification, an overhang may consist of anywhere from 1 nucleotideto 200 nucleotides (including every integer value in between).

The final chimeric nucleic acid molecule may be generated bysequentially assembling 2 or more building blocks at a time until allthe designated building blocks have been assembled. A working sample mayoptionally be subjected to a process for size selection or purificationor other selection or enrichment process between the performance of twoassembly steps. Alternatively, the final chimeric nucleic acid moleculemay be generated by assembling all the designated building blocks atonce in one step.

The methods of these experiments allow reassembly to occur among nucleicacids having a little or no homology. Additionally fusion points orcouplings can also occur in regions of low or no homology. The number ofresulting molecules that can be generated in according to thisexperiment is very large.

Rather than to physically generate and screen this large number ofpotential products in random order, it is appreciated that, optionallywith the aid of a computer, groupings of these potential products can benon-stochastically determined and furthermore ranked according to thepredicted the likelihood that desirable products are contained in eachgrouping. Accordingly it is appreciated according to this experimentthat computer modeling (“in silico”) or mental calculations orconsiderations (“in cranio”) may be useful to determine groupings all ofpotential reassembly products, where each such grouping is delineated bythe potential products that can be generated using one set (or a finiteset) of reagents and/or resulting from a one application (or a finitenumber of applications) of a method (or a finite number of methods)disclosed herein. Additionally the groupings can be ranked against eachother mentally or using computer modeling by predicting the number ofpotentially desirable or usable products in each grouping.

The grouping of potential products and the ranking of the groupings aredifferent facets of what is referred to herein as “triaging”, andspecifically “in silico triage” if performed using the aid of acomputer.

Examples of “structure-activity” considerations and serviceable computersoftware programs are abundant. The following examples are provided in anon-limiting fashion and are hereby incorporated by reference. MolecularSimulations Inc. of San Diego, Calif. is a subsidiary of Pharmacopeia,Inc. provides the following software programs that are useful for thisinvention: Gene Explorer™, ViewerPro™, SeqFold, Insight II, Biploymer,Homology, MODELER, Profiles-3D, Binding Site Analysis, and CFF.

In Vivo Shuffling

In an embodiment of in vivo shuffling, the mixed population of thespecific nucleic acid sequence is introduced into bacterial oreukaryotic cells under conditions such that at least two differentnucleic acid sequences are present in each host cell. Thepolynucleotides can be introduced into the host cells by a variety ofdifferent methods. The host cells can be transformed with the smallerpolynucleotides using methods known in the art, for example treatmentwith calcium chloride. If the polynucleotides are inserted into a phagegenome, the host cell can be transfected with the recombinant phagegenome having the specific nucleic acid sequences. Alternatively, thenucleic acid sequences can be introduced into the host cell usingelectroporation, transfection, lipofection, biolistics, conjugation, andthe like.

In general, in this embodiment, the specific nucleic acids sequenceswill be present in vectors which are capable of stably replicating thesequence in the host cell. In addition, it is contemplated that thevectors will encode a marker gene such that host cells having the vectorcan be selected. This ensures that the mutated specific nucleic acidsequence can be recovered after introduction into the host cell.However, it is contemplated that the entire mixed population of thespecific nucleic acid sequences need not be present on a vectorsequence. Rather only a sufficient number of sequences need be clonedinto vectors to ensure that after introduction of the polynucleotidesinto the host cells each host cell contains one vector having at leastone specific nucleic acid sequence present therein. It is alsocontemplated that rather than having a subset of the population of thespecific nucleic acids sequences cloned into vectors, this subset may bealready stably integrated into the host cell.

It has been found that when two polynucleotides which have regions ofidentity are inserted into the host cells homologous recombinationoccurs between the two polynucleotides. Such recombination between thetwo mutated specific nucleic acid sequences will result in theproduction of double or triple hybrids in some situations.

It has also been found that the frequency of recombination is increasedif some of the mutated specific nucleic acid sequences are present onlinear nucleic acid molecules. Therefore, in a preferred embodiment,some of the specific nucleic acid sequences are present on linearpolynucleotides.

After transformation, the host cell transformants are placed underselection to identify those host cell transformants which containmutated specific nucleic acid sequences having the qualities desired.For example, if increased resistance to a particular drug is desiredthen the transformed host cells may be subjected to increasedconcentrations of the particular drug and those transformants producingmutated proteins able to confer increased drug resistance will beselected. If the enhanced ability of a particular protein to bind to areceptor is desired, then expression of the protein can be induced fromthe transformants and the resulting protein assayed in a ligand bindingassay by methods known in the art to identify that subset of the mutatedpopulation which shows enhanced binding to the ligand. Alternatively,the protein can be expressed in another system to ensure properprocessing.

Once a subset of the first recombined specific nucleic acid sequences(daughter sequences) having the desired characteristics are identified,they are then subject to a second round of recombination.

In the second cycle of recombination, the recombined specific nucleicacid sequences may be mixed with the original mutated specific nucleicacid sequences (parent sequences) and the cycle repeated as describedabove. In this way a set of second recombined specific nucleic acidssequences can be identified which have enhanced characteristics orencode for proteins having enhanced properties. This cycle can berepeated a number of times as desired.

It is also contemplated that in the second or subsequent recombinationcycle, a backcross can be performed. A molecular backcross can beperformed by mixing the desired specific nucleic acid sequences with alarge number of the wild-type sequence, such that at least one wild-typenucleic acid sequence and a mutated nucleic acid sequence are present inthe same host cell after transformation. Recombination with thewild-type specific nucleic acid sequence will eliminate those neutralmutations that may affect unselected characteristics such asimmunogenicity but not the selected characteristics.

In another embodiment of this invention, it is contemplated that duringthe first round a subset of the specific nucleic acid sequences can begenerated as smaller polynucleotides by slowing or halting their PCRamplification prior to introduction into the host cell. The size of thepolynucleotides must be large enough to contain some regions of identitywith the other sequences so as to homologously recombine with the othersequences. The size of the polynucleotides will range from 0.03 kb to100 kb more preferably from 0.2 kb to 10 kb. It is also contemplatedthat in subsequent rounds, all of the specific nucleic acid sequencesother than the sequences selected from the previous round may beutilized to generate PCR polynucleotides prior to introduction into thehost cells.

The shorter polynucleotide sequences can be single-stranded ordouble-stranded. If the sequences were originally single-stranded andhave become double-stranded they can be denatured with heat, chemicalsor enzymes prior to insertion into the host cell. The reactionconditions suitable for separating the strands of nucleic acid are wellknown in the art.

The steps of this process can be repeated indefinitely, being limitedonly by the number of possible hybrids which can be achieved. After acertain number of cycles, all possible hybrids will have been achievedand further cycles are redundant.

In an embodiment the same mutated template nucleic acid is repeatedlyrecombined and the resulting recombinants selected for the desiredcharacteristic.

Therefore, the initial pool or population of mutated template nucleicacid is cloned into a vector capable of replicating in a bacteria suchas E. coli. The particular vector is not essential, so long as it iscapable of autonomous replication in E. coli. In a preferred embodiment,the vector is designed to allow the expression and production of anyprotein encoded by the mutated specific nucleic acid linked to thevector. It is also preferred that the vector contain a gene encoding fora selectable marker.

The population of vectors containing the pool of mutated nucleic acidsequences is introduced into the E. coli host cells. The vector nucleicacid sequences may be introduced by transformation, transfection orinfection in the case of phage. The concentration of vectors used totransform the bacteria is such that a number of vectors is introducedinto each cell. Once present in the cell, the efficiency of homologousrecombination is such that homologous recombination occurs between thevarious vectors. This results in the generation of hybrids (daughters)having a combination of mutations which differ from the original parentmutated sequences.

The host cells are then clonally replicated and selected for the markergene present on the vector. Only those cells having a plasmid will growunder the selection.

The host cells which contain a vector are then tested for the presenceof favorable mutations. Such testing may consist of placing the cellsunder selective pressure, for example, if the gene to be selected is animproved drug resistance gene. If the vector allows expression of theprotein encoded by the mutated nucleic acid sequence, then suchselection may include allowing expression of the protein so encoded,isolation of the protein and testing of the protein to determinewhether, for example, it binds with increased efficiency to the ligandof interest.

Once a particular daughter mutated nucleic acid sequence has beenidentified which confers the desired characteristics, the nucleic acidis isolated either already linked to the vector or separated from thevector. This nucleic acid is then mixed with the first or parentpopulation of nucleic acids and the cycle is repeated.

It has been shown that by this method nucleic acid sequences havingenhanced desired properties can be selected.

In an alternate embodiment, the first generation of hybrids are retainedin the cells and the parental mutated sequences are added again to thecells. Accordingly, the first cycle of Embodiment I is conducted asdescribed above. However, after the daughter nucleic acid sequences areidentified, the host cells containing these sequences are retained.

The parent mutated specific nucleic acid population, either aspolynucleotides or cloned into the same vector is introduced into thehost cells already containing the daughter nucleic acids. Recombinationis allowed to occur in the cells and the next generation ofrecombinants, or granddaughters are selected by the methods describedabove.

This cycle can be repeated a number of times until the nucleic acid orpeptide having the desired characteristics is obtained. It iscontemplated that in subsequent cycles, the population of mutatedsequences which are added to the preferred hybrids may come from theparental hybrids or any subsequent generation.

In an alternative embodiment, the invention provides a method ofconducting a “molecular” backcross of the obtained recombinant specificnucleic acid in order to eliminate any neutral mutations. Neutralmutations are those mutations which do not confer onto the nucleic acidor peptide the desired properties. Such mutations may however confer onthe nucleic acid or peptide undesirable characteristics. Accordingly, itis desirable to eliminate such neutral mutations. The method of thisinvention provide a means of doing so.

In this embodiment, after the hybrid nucleic acid, having the desiredcharacteristics, is obtained by the methods of the embodiments, thenucleic acid, the vector having the nucleic acid or the host cellcontaining the vector and nucleic acid is isolated.

The nucleic acid or vector is then introduced into the host cell with alarge excess of the wild-type nucleic acid. The nucleic acid of thehybrid and the nucleic acid of the wild-type sequence are allowed torecombine. The resulting recombinants are placed under the sameselection as the hybrid nucleic acid. Only those recombinants whichretained the desired characteristics will be selected. Any silentmutations which do not provide the desired characteristics will be lostthrough recombination with the wild-type DNA. This cycle can be repeateda number of times until all of the silent mutations are eliminated.

Thus the methods of this invention can be used in a molecular backcrossto eliminate unnecessary or silent mutations.

Utility

The in vivo recombination method of this invention can be performedblindly on a pool of unknown hybrids or alleles of a specificpolynucleotide or sequence. However, it is not necessary to know theactual DNA or RNA sequence of the specific polynucleotide.

The approach of using recombination within a mixed population of genescan be useful for the generation of any useful proteins, for example,interleukin I, antibodies, tPA and growth hormone. This approach may beused to generate proteins having altered specificity or activity. Theapproach may also be useful for the generation of hybrid nucleic acidsequences, for example, promoter regions, introns, exons, enhancersequences, 31 untranslated regions or 51 untranslated regions of genes.Thus this approach may be used to generate genes having increased ratesof expression. This approach may also be useful in the study ofrepetitive DNA sequences. Finally, this approach may be useful to mutateribozymes or aptamers.

Scaffold-like regions separating regions of diversity in proteins may beparticularly suitable for the methods of this invention. The conservedscaffold determines the overall folding by self-association, whiledisplaying relatively unrestricted loops that mediate the specificbinding. Examples of such scaffolds are the immunoglobulin beta barrel,and the four-helix bundle. The methods of this invention can be used tocreate scaffold-like proteins with various combinations of mutatedsequences for binding.

The equivalents of some standard genetic matings may also be performedby the methods of this invention. For example, a “molecular” backcrosscan be performed by repeated mixing of the hybrid's nucleic acid withthe wild-type nucleic acid while selecting for the mutations ofinterest. As in traditional breeding, this approach can be used tocombine phenotypes from different sources into a background of choice.It is useful, for example, for the removal of neutral mutations thataffect unselected characteristics (i.e. immunogenicity). Thus it can beuseful to determine which mutations in a protein are involved in theenhanced biological activity and which are not.

Peptide Display Methods

The present method can be used to shuffle, by in vitro and/or in vivorecombination by any of the disclosed methods, and in any combination,polynucleotide sequences selected by peptide display methods, wherein anassociated polynucleotide encodes a displayed peptide which is screenedfor a phenotype (e.g., for affinity for a predetermined receptor(ligand).

An increasingly important aspect of bio-pharmaceutical drug developmentand molecular biology is the identification of peptide structures,including the primary amino acid sequences, of peptides orpeptidomimetics that interact with biological macromolecules. one methodof identifying peptides that possess a desired structure or functionalproperty, such as binding to a predetermined biological macromolecule(e.g., a receptor), involves the screening of a large library orpeptides for individual library members which possess the desiredstructure or functional property conferred by the amino acid sequence ofthe peptide.

In addition to direct chemical synthesis methods for generating peptidelibraries, several recombinant DNA methods also have been reported. Onetype involves the display of a peptide sequence, antibody, or otherprotein on the surface of a bacteriophage particle or cell. Generally,in these methods each bacteriophage particle or cell serves as anindividual library member displaying a single species of displayedpeptide in addition to the natural bacteriophage or cell proteinsequences. Each bacteriophage or cell contains the nucleotide sequenceinformation encoding the particular displayed peptide sequence; thus,the displayed peptide sequence can be ascertained by nucleotide sequencedetermination of an isolated library member.

A well-known peptide display method involves the presentation of apeptide sequence on the surface of a filamentous bacteriophage,typically as a fusion with a bacteriophage coat protein. Thebacteriophage library can be incubated with an immobilized,predetermined macromolecule or small molecule (e.g., a receptor) so thatbacteriophage particles which present a peptide sequence that binds tothe immobilized macromolecule can be differentially partitioned fromthose that do not present peptide sequences that bind to thepredetermined macromolecule. The bacteriophage particles (i.e., librarymembers) which are bound to the immobilized macromolecule are thenrecovered and replicated to amplify the selected bacteriophagesub-population for a subsequent round of affinity enrichment and phagereplication. After several rounds of affinity enrichment and phagereplication, the bacteriophage library members that are thus selectedare isolated and the nucleotide sequence encoding the displayed peptidesequence is determined, thereby identifying the sequence(s) of peptidesthat bind to the predetermined macromolecule (e.g., receptor). Suchmethods are further described in PCT patent publications WO 91/17271, WO91/18980, WO 91/19818 and WO 93/08278.

The latter PCT publication describes a recombinant DNA method for thedisplay of peptide ligands that involves the production of a library offusion proteins with each fusion protein composed of a first polypeptideportion, typically comprising a variable sequence, that is available forpotential binding to a predetermined macromolecule, and a secondpolypeptide portion that binds to DNA, such as the DNA vector encodingthe individual fusion protein. When transformed host cells are culturedunder conditions that allow for expression of the fusion protein, thefusion protein binds to the DNA vector encoding it. Upon lysis of thehost cell, the fusion protein/vector DNA complexes can be screenedagainst a predetermined macromolecule in much the same way asbacteriophage particles are screened in the phage-based display system,with the replication and sequencing of the DNA vectors in the selectedfusion protein/vector DNA complexes serving as the basis foridentification of the selected library peptide sequence(s).

Other systems for generating libraries of peptides and like polymershave aspects of both the recombinant and in vitro chemical synthesismethods. In these hybrid methods, cell-free enzymatic machinery isemployed to accomplish the in vitro synthesis of the library members(i.e., peptides or polynucleotides). In one type of method, RNAmolecules with the ability to bind a predetermined protein or apredetermined dye molecule were selected by alternate rounds ofselection and PCR amplification (Tuerk and Gold, 1990; Ellington andSzostak, 1990). A similar technique was used to identify DNA sequenceswhich bind a predetermined human transcription factor (Thiesen and Bach,1990; Beaudry and Joyce, 1992; PCT patent publications WO 92/05258 andWO 92/14843). In a similar fashion, the technique of in vitrotranslation has been used to synthesize proteins of interest and hasbeen proposed as a method for generating large libraries of peptides.These methods which rely upon in vitro translation, generally comprisingstabilized polysome complexes, are described further in PCT patentpublications WO 88/08453, WO 90/05785, WO 90/07003, WO 91/02076, WO91/05058, and WO 92/02536. Applicants have described methods in whichlibrary members comprise a fusion protein having a first polypeptideportion with DNA binding activity and a second polypeptide portionhaving the library member unique peptide sequence; such methods aresuitable for use in cell-free in vitro selection formats, among others.

The displayed peptide sequences can be of varying lengths, typicallyfrom 3-5000 amino acids long or longer, frequently from 5-100 aminoacids long, and often from about 8-15 amino acids long. A library cancomprise library members having varying lengths of displayed peptidesequence, or may comprise library members having a fixed length ofdisplayed peptide sequence. Portions or all of the displayed peptidesequence(s) can be random, pseudorandom, defined set kernal, fixed, orthe like. The present display methods include methods for in vitro andin vivo display of single-chain antibodies, such as nascent scFv onpolysomes or scfv displayed on phage, which enable large-scale screeningof scfv libraries having broad diversity of variable region sequencesand binding specificities.

The present invention also provides random, pseudorandom, and definedsequence framework peptide libraries and methods for generating andscreening those libraries to identify useful compounds (e.g., peptides,including single-chain antibodies) that bind to receptor molecules orepitopes of interest or gene products that modify peptides or RNA in adesired fashion. The random, pseudorandom, and defined sequenceframework peptides are produced from libraries of peptide librarymembers that comprise displayed peptides or displayed single-chainantibodies attached to a polynucleotide template from which thedisplayed peptide was synthesized. The mode of attachment may varyaccording to the specific embodiment of the invention selected, and caninclude encapsulation in a phage particle or incorporation in a cell.

A method of affinity enrichment allows a very large library of peptidesand single-chain antibodies to be screened and the polynucleotidesequence encoding the desired peptide(s) or single-chain antibodies tobe selected. The polynucleotide can then be isolated and shuffled torecombine combinatorially the amino acid sequence of the selectedpeptide(s) (or predetermined portions thereof) or single-chainantibodies (or just VHI, VLI or CDR portions thereof). Using thesemethods, one can identify a peptide or single-chain antibody as having adesired binding affinity for a molecule and can exploit the process ofshuffling to converge rapidly to a desired high-affinity peptide orscfv. The peptide or antibody can then be synthesized in bulk byconventional means for any suitable use (e.g., as a therapeutic ordiagnostic agent).

A significant advantage of the present invention is that no priorinformation regarding an expected ligand structure is required toisolate peptide ligands or antibodies of interest. The peptideidentified can have biological activity, which is meant to include atleast specific binding affinity for a selected receptor molecule and, insome instances, will further include the ability to block the binding ofother compounds, to stimulate or inhibit metabolic pathways, to act as asignal or messenger, to stimulate or inhibit cellular activity, and thelike.

The present invention also provides a method for shuffling a pool ofpolynucleotide sequences selected by affinity screening a library ofpolysomes displaying nascent peptides (including single-chainantibodies) for library members which bind to a predetermined receptor(e.g., a mammalian proteinaceous receptor such as, for example, apeptidergic hormone receptor, a cell surface receptor, an intracellularprotein which binds to other protein(s) to form intracellular proteincomplexes such as hetero-dimers and the like) or epitope (e.g., animmobilized protein, glycoprotein, oligosaccharide, and the like).

Polynucleotide sequences selected in a first selection round (typicallyby affinity selection for binding to a receptor (e.g., a ligand)) by anyof these methods are pooled and the pool(s) is/are shuffled by in vitroand/or in vivo recombination to produce a shuffled pool comprising apopulation of recombined selected polynucleotide sequences. Therecombined selected polynucleotide sequences are subjected to at leastone subsequent selection round. The polynucleotide sequences selected inthe subsequent selection round(s) can be used directly, sequenced,and/or subjected to one or more additional rounds of shuffling andsubsequent selection. Selected sequences can also be back-crossed withpolynucleotide sequences encoding neutral sequences (i.e., havinginsubstantial functional effect on binding), such as for example byback-crossing with a wild-type or naturally-occurring sequencesubstantially identical to a selected sequence to produce native-likefunctional peptides, which may be less immunogenic. Generally, duringback-crossing subsequent selection is applied to retain the property ofbinding to the predetermined receptor (ligand).

Prior to or concomitant with the shuffling of selected sequences, thesequences can be mutagenized. In one embodiment, selected librarymembers are cloned in a prokaryotic vector (e.g., plasmid, phagemid, orbacteriophage) wherein a collection of individual colonies (or plaques)representing discrete library members are produced. Individual selectedlibrary members can then be manipulated (e.g., by site-directedmutagenesis, cassette mutagenesis, chemical mutagenesis, PCRmutagenesis, and the like) to generate a collection of library membersrepresenting a kernal of sequence diversity based on the sequence of theselected library member. The sequence of an individual selected librarymember or pool can be manipulated to incorporate random mutation,pseudorandom mutation, defined kernal mutation (i.e., comprising variantand invariant residue positions and/or comprising variant residuepositions which can comprise a residue selected from a defined subset ofamino acid residues), codon-based mutation, and the like, eithersegmentally or over the entire length of the individual selected librarymember sequence. The mutagenized selected library members are thenshuffled by in vitro and/or in vivo recombinatorial shuffling asdisclosed herein.

The invention also provides peptide libraries comprising a plurality ofindividual library members of the invention, wherein (1) each individuallibrary member of said plurality comprises a sequence produced byshuffling of a pool of selected sequences, and (2) each individuallibrary member comprises a variable peptide segment sequence orsingle-chain antibody segment sequence which is distinct from thevariable peptide segment sequences or single-chain antibody sequences ofother individual library members in said plurality (although somelibrary members may be present in more than one copy per library due touneven amplification, stochastic probability, or the like).

The invention also provides a product-by-process, wherein selectedpolynucleotide sequences having (or encoding a peptide having) apredetermined binding specificity are formed by the process of: (1)screening a displayed peptide or displayed single-chain antibody libraryagainst a predetermined receptor (e.g., ligand) or epitope (e.g.,antigen macromolecule) and identifying and/or enriching library memberswhich bind to the predetermined receptor or epitope to produce a pool ofselected library members, (2) shuffling by recombination the selectedlibrary members (or amplified or cloned copies thereof) which binds thepredetermined epitope and has been thereby isolated and/or enriched fromthe library to generate a shuffled library, and (3) screening theshuffled library against the predetermined receptor (e.g., ligand) orepitope (e.g., antigen macromolecule) and identifying and/or enrichingshuffled library members which bind to the predetermined receptor orepitope to produce a pool of selected shuffled library members.

Antibody Display and Screening Methods

The present method can be used to shuffle, by in vitro and/or in vivorecombination by any of the disclosed methods, and in any combination,polynucleotide sequences selected by antibody display methods, whereinan associated polynucleotide encodes a displayed antibody which isscreened for a phenotype (e.g., for affinity for binding a predeterminedantigen (ligand).

Various molecular genetic approaches have been devised to capture thevast immunological repertoire represented by the extremely large numberof distinct variable regions which can be present in immunoglobulinchains. The naturally-occurring germ line immunoglobulin heavy chainlocus is composed of separate tandem arrays of variable segment geneslocated upstream of a tandem array of diversity segment genes, which arethemselves located upstream of a tandem array of joining (i) regiongenes, which are located upstream of the constant region genes. During Blymphocyte development, V-D-J rearrangement occurs wherein a heavy chainvariable region gene (VH) is formed by rearrangement to form a fused Dsegment followed by rearrangement with a V segment to form a V-D-Jjoined product gene which, if productively rearranged, encodes afunctional variable region (VH) of a heavy chain. Similarly, light chainloci rearrange one of several V segments with one of several J segmentsto form a gene encoding the variable region (VL) of a light chain.

The vast repertoire of variable regions possible in immunoglobulinsderives in part from the numerous combinatorial possibilities of joiningV and i segments (and, in the case of heavy chain loci, D segments)during rearrangement in B cell development. Additional sequencediversity in the heavy chain variable regions arises from non-uniformrearrangements of the D segments during V-D-J joining and from N regionaddition. Further, antigen-selection of specific B cell clones selectsfor higher affinity variants having non-germline mutations in one orboth of the heavy and light chain variable regions; a phenomenonreferred to as “affinity maturation” or “affinity sharpening”.Typically, these “affinity sharpening” mutations cluster in specificareas of the variable region, most commonly in thecomplementarity-determining regions (CDRs).

In order to overcome many of the limitations in producing andidentifying high-affinity immunoglobulins through antigen-stimulated βcell development (i.e., immunization), various prokaryotic expressionsystems have been developed that can be manipulated to producecombinatorial antibody libraries which may be screened for high-affinityantibodies to specific antigens. Recent advances in the expression ofantibodies in Escherichia coli and bacteriophage systems (see“alternative peptide display methods”, infra) have raised thepossibility that virtually any specificity can be obtained by eithercloning antibody genes from characterized hybridomas or by de novoselection using antibody gene libraries (e.g., from Ig cDNA).

Combinatorial libraries of antibodies have been generated inbacteriophage lambda expression systems which may be screened asbacteriophage plaques or as colonies of lysogens (Huse et al, 1989);Caton and Koprowski, 1990; Mullinax et al, 1990; Persson et al, 1991).Various embodiments of bacteriophage antibody display libraries andlambda phage expression libraries have been described (Kang et al, 1991;Clackson et al, 1991; McCafferty et al, 1990; Burton et al, 1991;Hoogenboom et al, 1991; Chang et al, 1991; Breitling et al, 1991; Markset al, 1991, p. 581; Barbas et al, 1992; Hawkins and Winter, 1992; Markset al, 1992, p. 779; Marks et al, 1992, p. 16007; and Lowman et al,1991; Lerner et al, 1992; all incorporated herein by reference).Typically, a bacteriophage antibody display library is screened with areceptor (e.g., polypeptide, carbohydrate, glycoprotein, nucleic acid)that is immobilized (e.g., by covalent linkage to a chromatography resinto enrich for reactive phage by affinity chromatography) and/or labeled(e.g., to screen plaque or colony lifts).

One particularly advantageous approach has been the use of so-calledsingle-chain fragment variable (scfv) libraries (Marks et al, 1992, p.779; Winter and Milstein, 1991; Clackson et al, 1991; Marks et al, 1991,p. 581; Chaudhary et al, 1990; Chiswell et al, 1992; McCafferty et al,1990; and Huston et al, 1988). Various embodiments of scfv librariesdisplayed on bacteriophage coat proteins have been described.

Beginning in 1988, single-chain analogues of Fv fragments and theirfusion proteins have been reliably generated by antibody engineeringmethods. The first step generally involves obtaining the genes encodingVH and VL domains with desired binding properties; these V genes may beisolated from a specific hybridoma cell line, selected from acombinatorial V-gene library, or made by V gene synthesis. Thesingle-chain Fv is formed by connecting the component V genes with anoligonucleotide that encodes an appropriately designed linker peptide,such as (Gly-Gly-Gly-Gly-Ser)3 or equivalent linker peptide(s). Thelinker bridges the C-terminus of the first V region and N-terminus ofthe second, ordered as either VH-linker-VL or VL-linker-VH′ Inprinciple, the scfv binding site can faithfully replicate both theaffinity and specificity of its parent antibody combining site.

Thus, scfv fragments are comprised of VH and VL domains linked into asingle polypeptide chain by a flexible linker peptide. After the scfvgenes are assembled, they are cloned into a phagemid and expressed atthe tip of the M13 phage (or similar filamentous bacteriophage) asfusion proteins with the bacteriophage PIII (gene 3) coat protein.Enriching for phage expressing an antibody of interest is accomplishedby panning the recombinant phage displaying a population scfv forbinding to a predetermined epitope (e.g., target antigen, receptor).

The linked polynucleotide of a library member provides the basis forreplication of the library member after a screening or selectionprocedure, and also provides the basis for the determination, bynucleotide sequencing, of the identity of the displayed peptide sequenceor VH and VL amino acid sequence. The displayed peptide (s) orsingle-chain antibody (e.g., scfv) and/or its VH and VL domains or theirCDRs can be cloned and expressed in a suitable expression system. Oftenpolynucleotides encoding the isolated VH and VL domains will be ligatedto polynucleotides encoding constant regions (CH and CL) to formpolynucleotides encoding complete antibodies (e.g., chimeric orfully-human), antibody fragments, and the like. Often polynucleotidesencoding the isolated CDRs will be grafted into polynucleotides encodinga suitable variable region framework (and optionally constant regions)to form polynucleotides encoding complete antibodies (e.g., humanized orfully-human), antibody fragments, and the like. Antibodies can be usedto isolate preparative quantities of the antigen by immunoaffinitychromatography. Various other uses of such antibodies are to diagnoseand/or stage disease (e.g., neoplasia) and for therapeutic applicationto treat disease, such as for example: neoplasia, autoimmune disease,AIDS, cardiovascular disease, infections, and the like.

Various methods have been reported for increasing the combinatorialdiversity of a scfv library to broaden the repertoire of binding species(idiotype spectrum) The use of PCR has permitted the variable regions tobe rapidly cloned either from a specific hybridoma source or as a genelibrary from non-immunized cells, affording combinatorial diversity inthe assortment of VH and VL cassettes which can be combined.Furthermore, the VH and VL cassettes can themselves be diversified, suchas by random, pseudorandom, or directed mutagenesis. Typically, VH andVL cassettes are diversified in or near the complementarity-determiningregions (CDRS), often the third CDR, CDR3. Enzymatic inverse PCRmutagenesis has been shown to be a simple and reliable method forconstructing relatively large libraries of scfv site-directed hybrids(Stemmer et al, 1993), as has error-prone PCR and chemical mutagenesis(Deng et al, 1994). Riechmann (Riechmann et al, 1993) showedsemi-rational design of an antibody scfv fragment using site-directedrandomization by degenerate oligonucleotide PCR and subsequent phagedisplay of the resultant scfv hybrids. Barbas (Barbas et al, 1992)attempted to circumvent the problem of limited repertoire sizesresulting from using biased variable region sequences by randomizing thesequence in a synthetic CDR region of a human tetanus toxoid-bindingFab.

CDR randomization has the potential to create approximately 1×10²⁰ CDRsfor the heavy chain CDR3 alone, and a roughly similar number of variantsof the heavy chain CDR1 and CDR2, and light chain CDR1-3 variants. Takenindividually or together, the combination possibilities of CDRrandomization of heavy and/or light chains requires generating aprohibitive number of bacteriophage clones to produce a clone libraryrepresenting all possible combinations, the vast majority of which willbe non-binding. Generation of such large numbers of primarytransformants is not feasible with current transformation technology andbacteriophage display systems. For example, Barbas (Barbas et al, 1992)only generated 5×10⁷ transformants, which represents only a tinyfraction of the potential diversity of a library of thoroughlyrandomized CDRS.

Despite these substantial limitations, bacteriophage. display of scfvhave already yielded a variety of useful antibodies and antibody fusionproteins. A bispecific single chain antibody has been shown to mediateefficient tumor cell lysis (Gruber et al, 1994). Intracellularexpression of an anti-Rev scfv has been shown to inhibit HIV-1 virusreplication in vitro (Duan et al, 1994), and intracellular expression ofan anti-p21rar, scfv has been shown to inhibit meiotic maturation ofXenopus oocytes (Biocca et al, 1993). Recombinant scfv which can be usedto diagnose HIV infection have also been reported, demonstrating thediagnostic utility of scfv (Lilley et al, 1994). Fusion proteins whereinan scFv is linked to a second polypeptide, such as a toxin orfibrinolytic activator protein, have also been reported (Holvost et al,1992; Nicholls et al, 1993).

If it were possible to generate scfv libraries having broader antibodydiversity and overcoming many of the limitations of conventional CDRmutagenesis and randomization methods which can cover only a very tinyfraction of the potential sequence combinations, the number and qualityof scfv antibodies suitable for therapeutic and diagnostic use could bevastly improved. To address this, the in vitro and in vivo shufflingmethods of the invention are used to recombine CDRs which have beenobtained (typically via PCR amplification or cloning) from nucleic acidsobtained from selected displayed antibodies. Such displayed antibodiescan be displayed on cells, on bacteriophage particles, on polysomes, orany suitable antibody display system wherein the antibody is associatedwith its encoding nucleic acid(s). In a variation, the CDRs areinitially obtained from mRNA (or cDNA) from antibody-producing cells(e.g., plasma cells/splenocytes from an immunized wild-type mouse, ahuman, or a transgenic mouse capable of making a human antibody as in WO92/03918, WO 93/12227, and WO 94/25585), including hybridomas derivedtherefrom.

Polynucleotide sequences selected in a first selection round (typicallyby affinity selection for displayed antibody binding to an antigen(e.g., a ligand) by any of these methods are pooled and the pool(s)is/are shuffled by in vitro and/or in vivo recombination, especiallyshuffling of CDRs (typically shuffling heavy chain CDRs with other heavychain CDRs and light chain CDRs with other light chain CDRs) to producea shuffled pool comprising a population of recombined selectedpolynucleotide sequences. The recombined selected polynucleotidesequences are expressed in a selection format as a displayed antibodyand subjected to at least one subsequent selection round. Thepolynucleotide sequences selected in the subsequent selection round(s)can be used directly, sequenced, and/or subjected to one or moreadditional rounds of shuffling and subsequent selection until anantibody of the desired binding affinity is obtained. Selected sequencescan also be back-crossed with polynucleotide sequences encoding neutralantibody framework sequences (i.e., having insubstantial functionaleffect on antigen binding), such as for example by back-crossing with ahuman variable region framework to produce human-like sequenceantibodies. Generally, during back-crossing subsequent selection isapplied to retain the property of binding to the predetermined antigen.

Alternatively, or in combination with the noted variations, the valencyof the target epitope may be varied to control the average bindingaffinity of selected scfv library members. The target epitope can bebound to a surface or substrate at varying densities, such as byincluding a competitor epitope, by dilution, or by other method known tothose in the art. A high density (valency) of predetermined epitope canbe used to enrich for scfv library members which have relatively lowaffinity, whereas a low density (valency) can preferentially enrich forhigher affinity scfv library members.

For generating diverse variable segments, a collection of syntheticoligonucleotides encoding random, pseudorandom, or a defined sequencekernal set of peptide sequences can be inserted by ligation into apredetermined site (e.g., a CDR). Similarly, the sequence diversity ofone or more CDRs of the single-chain antibody cassette(s) can beexpanded by mutating the CDR(s) with site-directed mutagenesis,CDR-replacement, and the like. The resultant DNA molecules can bepropagated in a host for cloning and amplification prior to shuffling,or can be used directly (i.e., may avoid loss of diversity which mayoccur upon propagation in a host cell) and the selected library memberssubsequently shuffled.

Displayed peptide/polynucleotide complexes (library members) whichencode a variable segment peptide sequence of interest or a single-chainantibody of interest are selected from the library by an affinityenrichment technique. This is accomplished by means of a immobilizedmacromolecule or epitope specific for the peptide sequence of interest,such as a receptor, other macromolecule, or other epitope species.Repeating the affinity selection procedure provides an enrichment oflibrary members encoding the desired sequences, which may then beisolated for pooling and shuffling, for sequencing, and/or for furtherpropagation and affinity enrichment.

The library members without the desired specificity are removed bywashing. The degree and stringency of washing required will bedetermined for each peptide sequence or single-chain antibody ofinterest and the immobilized predetermined macromolecule or epitope. Acertain degree of control can be exerted over the bindingcharacteristics of the nascent peptide/DNA complexes recovered byadjusting the conditions of the binding incubation and the subsequentwashing. The temperature, pH, ionic strength, divalent cationsconcentration, and the volume and duration of the washing will selectfor nascent peptide/DNA complexes within particular ranges of affinityfor the immobilized macromolecule. Selection based on slow dissociationrate, which is usually predictive of high affinity, is often the mostpractical route. This may be done either by continued incubation in thepresence of a saturating amount of free predetermined macromolecule, orby increasing the volume, number, and length of the washes. In eachcase, the rebinding of dissociated nascent peptide/DNA or peptide/RNAcomplex is prevented, and with increasing time, nascent peptide/DNA orpeptide/RNA complexes of higher and higher affinity are recovered.

Additional modifications of the binding and washing procedures may beapplied to find peptides with special characteristics. The affinities ofsome peptides are dependent on ionic strength or cation concentration.This is a useful characteristic for peptides that will be used inaffinity purification of various proteins when gentle conditions forremoving the protein from the peptides are required.

One variation involves the use of multiple binding targets (multipleepitope species, multiple receptor species), such that a scfv librarycan be simultaneously screened for a multiplicity of scfv which havedifferent binding specificities. Given that the size of a scfv libraryoften limits the diversity of potential scfv sequences, it is typicallydesirable to us scfv libraries of as large a size as possible. The timeand economic considerations of generating a number of very largepolysome scFv-display libraries can become prohibitive. To avoid thissubstantial problem, multiple predetermined epitope species (receptorspecies) can be concomitantly screened in a single library, orsequential screening against a number of epitope species can be used. Inone variation, multiple target epitope species, each encoded on aseparate bead (or subset of beads), can be mixed and incubated with apolysome-display scfv library under suitable binding conditions. Thecollection of beads, comprising multiple epitope species, can then beused to isolate, by affinity selection, scfv library members. Generally,subsequent affinity screening rounds can include the same mixture ofbeads, subsets thereof, or beads containing only one or two individualepitope species. This approach affords efficient screening, and iscompatible with laboratory automation, batch processing, and highthroughput screening methods.

A variety of techniques can be used in the present invention todiversify a peptide library or single-chain antibody library, or todiversify, prior to or concomitant with shuffling, around variablesegment peptides found in early rounds of panning to have sufficientbinding activity to the predetermined macromolecule or epitope. In oneapproach, the positive selected peptide/polynucleotide complexes (thoseidentified in an early round of affinity enrichment) are sequenced todetermine the identity of the active peptides. Oligonucleotides are thensynthesized based on these active peptide sequences, employing a lowlevel of all bases incorporated at each step to produce slightvariations of the primary oligonucleotide sequences. This mixture of(slightly) degenerate oligonucleotides is then cloned into the variablesegment sequences at the appropriate locations. This method producessystematic, controlled variations of the starting peptide sequences,which can then be shuffled. It requires, however, that individualpositive nascent peptide/polynucleotide complexes be sequenced beforemutagenesis, and thus is useful for expanding the diversity of smallnumbers of recovered complexes and selecting variants having higherbinding affinity and/or higher binding specificity. In a variation,mutagenic PCR amplification of positive selected peptide/polynucleotidecomplexes (especially of the variable region sequences, theamplification products of which are shuffled in vitro and/or in vivo andone or more additional rounds of screening is done prior to sequencing.The same general approach can be employed with single-chain antibodiesin order to expand the diversity and enhance the bindingaffinity/specificity, typically by diversifying CDRs or adjacentframework regions prior to or concomitant with shuffling. If desired,shuffling reactions can be spiked with mutagenic oligonucleotidescapable of in vitro recombination with the selected library members canbe included. Thus, mixtures of synthetic oligonucleotides and PCRproduced polynucleotides (synthesized by error-prone or high-fidelitymethods) can be added to the in vitro shuffling mix and be incorporatedinto resulting shuffled library members (shufflants).

The present invention of shuffling enables the generation of a vastlibrary of CDR-variant single-chain antibodies. One way to generate suchantibodies is to insert synthetic CDRs into the single-chain antibodyand/or CDR randomization prior to or concomitant with shuffling. Thesequences of the synthetic CDR cassettes are selected by referring toknown sequence data of human CDR and are selected in the discretion ofthe practitioner according to the following guidelines: synthetic CDRswill have at least 40 percent positional sequence identity to known CDRsequences, and preferably will have at least 50 to 70 percent positionalsequence identity to known CDR sequences. For example, a collection ofsynthetic CDR sequences can be generated by synthesizing a collection ofoligonucleotide sequences on the basis of naturally-occurring human CDRsequences listed in Kabat (Kabat et al, 1991); the pool (s) of syntheticCDR sequences are calculated to encode CDR peptide sequences having atleast 40 percent sequence identity to at least one knownnaturally-occurring human CDR sequence. Alternatively, a collection ofnaturally-occurring CDR sequences may be compared to generate consensussequences so that amino acids used at a residue position frequently(i.e., in at least 5 percent of known CDR sequences) are incorporatedinto the synthetic CDRs at the corresponding position(s). Typically,several (e.g., 3 to about 50) known CDR sequences are compared andobserved natural sequence variations between the known CDRs aretabulated, and a collection of oligonucleotides encoding CDR peptidesequences encompassing all or most permutations of the observed naturalsequence variations is synthesized. For example but not for limitation,if a collection of human VH CDR sequences have carboxy-terminal aminoacids which are either Tyr, Val, Phe, or Asp, then the pool(s) ofsynthetic CDR oligonucleotide sequences are designed to allow thecarboxy-terminal CDR residue to be any of these amino acids. In someembodiments, residues other than those which naturally-occur at aresidue position in the collection of CDR sequences are incorporated:conservative amino acid substitutions are frequently incorporated and upto 5 residue positions may be varied to incorporate non-conservativeamino acid substitutions as compared to known naturally-occurring CDRsequences. Such CDR sequences can be used in primary library members(prior to first round screening) and/or can be used to spike in vitroshuffling reactions of selected library member sequences. Constructionof such pools of defined and/or degenerate sequences will be readilyaccomplished by those of ordinary skill in the art.

The collection of synthetic CDR sequences comprises at least one memberthat is not known to be a naturally-occurring CDR sequence. It is withinthe discretion of the practitioner to include or not include a portionof random or pseudorandom sequence corresponding to N region addition inthe heavy chain CDR; the N region sequence ranges from 1 nucleotide toabout 4 nucleotides occurring at V-D and D-J junctions. A collection ofsynthetic heavy chain CDR sequences comprises at least about 100 uniqueCDR sequences, typically at least about 1,000 unique CDR sequences,preferably at least about 10,000 unique CDR sequences, frequently morethan 50,000 unique CDR sequences; however, usually not more than about1×10 6 unique CDR sequences are included in the collection, althoughoccasionally 1×107 to 1×108 unique CDR sequences are present, especiallyif conservative amino acid substitutions are permitted at positionswhere the conservative amino acid substituent is not present or is rare(i.e., less than 0.1 percent) in that position in naturally-occurringhuman CDRS. In general, the number of unique CDR sequences included in alibrary should not exceed the expected number of primary transformantsin the library by more than a factor of 10. Such single-chain antibodiesgenerally bind of about at least 1×10 m-, preferably with an affinity ofabout at least 5×10⁷ M-1, more preferably with an affinity of at least1×10⁸ M-1 to 1×10⁹ M-1 or more, sometimes up to 1×10¹⁰ M-1 or more.Frequently, the predetermined antigen is a human protein, such as forexample a human cell surface antigen (e.g., CD4, CD8, IL-2 receptor, EGFreceptor, PDGF receptor), other human biological macromolecule (e.g.,thrombomodulin, protein C, carbohydrate antigen, sialyl Lewis antigen,Lselectin), or nonhuman disease associated macromolecule (e.g.,bacterial LPS, virion capsid protein or envelope glycoprotein) and thelike.

High affinity single-chain antibodies of the desired specificity can beengineered and expressed in a variety of systems. For example, scfv havebeen produced in plants (Firek et al, 1993) and can be readily made inprokaryotic systems (Owens and Young, 1994; Johnson and Bird, 1991).Furthermore, the single-chain antibodies can be used as a basis forconstructing whole antibodies or various fragments thereof(Kettleborough et al, 1994). The variable region encoding sequence maybe isolated (e.g., by PCR amplification or subcloning) and spliced to asequence encoding a desired human constant region to encode a humansequence antibody more suitable for human therapeutic uses whereimmunogenicity is preferably minimized. The polynucleotide(s) having theresultant fully human encoding sequence(s) can be expressed in a hostcell (e.g., from an expression vector in a mammalian cell) and purifiedfor pharmaceutical formulation.

The DNA expression constructs will typically include an expressioncontrol DNA sequence operably linked to the coding sequences, includingnaturally-associated or heterologous promoter regions. Preferably, theexpression control sequences will be eukaryotic promoter systems invectors capable of transforming or transfecting eukaryotic host cells.Once the vector has been incorporated into the appropriate host, thehost is maintained under conditions suitable for high level expressionof the nucleotide sequences, and the collection and purification of themutant′ “engineered” antibodies.

As stated previously, the DNA sequences will be expressed in hosts afterthe sequences have been operably linked to an expression controlsequence (i.e., positioned to ensure the transcription and translationof the structural gene). These expression vectors are typicallyreplicable in the host organisms either as episomes or as an integralpart of the host chromosomal DNA. Commonly, expression vectors willcontain selection markers, e.g., tetracycline or neomycin, to permitdetection of those cells transformed with the desired DNA sequences(see, e.g., U.S. Pat. No. 4,704,362, which is incorporated herein byreference).

In addition to eukaryotic microorganisms such as yeast, mammalian tissuecell culture may also be used to produce the polypeptides of the presentinvention (see Winnacker, 1987), which is incorporated herein byreference). Eukaryotic cells are actually preferred, because a number ofsuitable host cell lines capable of secreting intact immunoglobulinshave been developed in the art, and include the CHO cell lines, variousCOS cell lines, HeLa cells, and myeloma cell lines, but preferablytransformed Bcells or hybridomas. Expression vectors for these cells caninclude expression control sequences, such as an origin of replication,a promoter, an enhancer (Queen et al, 1986), and necessary processinginformation sites, such as ribosome binding sites, RNA splice sites,polyadenylation sites, and transcriptional terminator sequences.Preferred expression control sequences are promoters derived fromimmunoglobulin genes, cytomegalovirus, SV40, Adenovirus, BovinePapilloma Virus, and the like.

Eukaryotic DNA transcription can be increased by inserting an enhancersequence into the vector. Enhancers are cis-acting sequences of between10 to 300 bp that increase transcription by a promoter. Enhancers caneffectively increase transcription when either 51 or 31 to thetranscription unit. They are also effective if located within an intronor within the coding sequence itself. Typically, viral enhancers areused, including SV40 enhancers, cytomegalovirus enhancers, polyomaenhancers, and adenovirus enhancers. Enhancer sequences from mammaliansystems are also commonly used, such as the mouse immunoglobulin heavychain enhancer.

Mammalian expression vector systems will also typically include aselectable marker gene. Examples of suitable markers include, thedihydrofolate reductase gene (DHFR), the thymidine kinase gene (TK), orprokaryotic genes conferring drug resistance. The first two marker genesprefer the use of mutant cell lines that lack the ability to growwithout the addition of thymidine to the growth medium. Transformedcells can then be identified by their ability to grow onnon-supplemented media. Examples of prokaryotic drug resistance genesuseful as markers include genes conferring resistance to G418,mycophenolic acid and hygromycin.

The vectors containing the DNA segments of interest can be transferredinto the host cell by well-known methods, depending on the type ofcellular host. For example, calcium chloride transfection is commonlyutilized for prokaryotic cells, whereas calcium phosphate treatment.lipofection, or electroporation may be used for other cellular hosts.Other methods used to transform mammalian cells include the use ofPolybrene, protoplast fusion, liposomes, electroporation, andmicro-injection (see, generally, Sambrook et al, 1982 and 1989).

Once expressed, the antibodies, individual mutated immunoglobulinchains, mutated antibody fragments, and other immunoglobulinpolypeptides of the invention can be purified according to standardprocedures of the art, including ammonium sulfate precipitation,fraction column chromatography, gel electrophoresis and the like (see,generally, Scopes, 1982). Once purified, partially or to homogeneity asdesired, the polypeptides may then be used therapeutically or indeveloping and performing assay procedures, immunofluorescent stainings,and the like (see, generally, Lefkovits and Pernis, 1979 and 1981;Lefkovits, 1997).

The antibodies generated by the method of the present invention can beused for diagnosis and therapy. By way of illustration and notlimitation, they can be used to treat cancer, autoimmune diseases, orviral infections. For treatment of cancer, the antibodies will typicallybind to an antigen expressed preferentially on cancer cells, such aserbB-2, CEA, CD33, and many other antigens and binding members wellknown to those skilled in the art.

End-Selection

This invention provides a method for selecting a subset ofpolynucleotides from a starting set of polynucleotides, which method isbased on the ability to discriminate one or more selectable features (orselection markers) present anywhere in a working polynucleotide, so asto allow one to perform selection for (positive selection) &/or against(negative selection) each selectable polynucleotide. In a preferredaspect, a method is provided termed end-selection, which method is basedon the use of a selection marker located in part or entirely in aterminal region of a selectable polynucleotide, and such a selectionmarker may be termed an “end-selection marker”.

End-selection may be based on detection of naturally occurring sequencesor on detection of sequences introduced experimentally (including by anymutagenesis procedure mentioned herein and not mentioned herein) or onboth, even within the same polynucleotide. An end-selection marker canbe a structural selection marker or a functional selection marker orboth a structural and a functional selection marker. An end-selectionmarker may be comprised of a polynucleotide sequence or of a polypeptidesequence or of any chemical structure or of any biological orbiochemical tag, including markers that can be selected using methodsbased on the detection of radioactivity, of enzymatic activity, offluorescence, of any optical feature, of a magnetic property (e.g. usingmagnetic beads), of immunoreactivity, and of hybridization.

End-selection may be applied in combination with any method serviceablefor performing mutagenesis. Such mutagenesis methods include, but arenot limited to, methods described herein (supra and infra). Such methodsinclude, by way of non-limiting exemplification, any method that may bereferred herein or by others in the art by any of the following terms:“saturation mutagenesis”, “shuffling”, “recombination”, “reassembly”,“error-prone PCR”, “assembly PCR”, “sexual PCR”, “crossover PCR”,“oligonucleotide primer-directed mutagenesis”, “recursive (&/orexponential) ensemble mutagenesis (see Arkin and Youvan, 1992)”,“cassette mutagenesis”, “in vivo mutagenesis”, and “in vitromutagenesis”. Moreover, end-selection may be performed on moleculesproduced by any mutagenesis &/or amplification method (see, e.g.,Arnold, 1993; Caldwell and Joyce, 1992; Stemmer, 1994; following whichmethod it is desirable to select for (including to screen for thepresence of) desirable progeny molecules.

In addition, end-selection may be applied to a polynucleotide apart fromany mutagenesis method. In a preferred embodiment, end-selection, asprovided herein, can be used in order to facilitate a cloning step, suchas a step of ligation to another polynucleotide (including ligation to avector). This invention thus provides for end-selection as a serviceablemeans to facilitate library construction, selection &/or enrichment fordesirable polynucleotides, and cloning in general.

In a particularly preferred embodiment, end-selection can be based on(positive) selection for a polynucleotide; alternatively end-selectioncan be based on (negative) selection against a polynucleotide; andalternatively still, end-selection can be based on both (positive)selection for, and on (negative) selection against, a polynucleotide.End-selection, along with other methods of selection &/or screening, canbe performed in an iterative fashion, with any combination of like orunlike selection &/or screening methods and serviceable mutagenesismethods, all of which can be performed in an iterative fashion and inany order, combination, and permutation.

It is also appreciated that, according to one embodiment of thisinvention, end-selection may also be used to select a polynucleotide isat least in part: circular (e.g. a plasmid or any other circular vectoror any other polynucleotide that is partly circular), &/or branched,&/or modified or substituted with any chemical group or moiety. Inaccord with this embodiment, a polynucleotide may be a circular moleculecomprised of an intermediate or central region, which region is flankedon a 5′ side by a 5′ flanking region (which, for the purpose ofend-selection, serves in like manner to a 5′ terminal region of anon-circular polynucleotide) and on a 3′ side by a 3′ terminal region(which, for the purpose of end-selection, serves in like manner to a 3′terminal region of a non-circular polynucleotide). As used in thisnon-limiting exemplification, there may be sequence overlap between anytwo regions or even among all three regions.

In one non-limiting aspect of this invention, end-selection of a linearpolynucleotide is performed using a general approach based on thepresence of at least one end-selection marker located at or near apolynucleotide end or terminus (that can be either a 5′ end or a 3′end). In one particular non-limiting exemplification, end-selection isbased on selection for a specific sequence at or near a terminus suchas, but not limited to, a sequence recognized by an enzyme thatrecognizes a polynucleotide sequence. An enzyme that recognizes andcatalyzes a chemical modification of a polynucleotide is referred toherein as a polynucleotide-acting enzyme. In a preferred embodiment,serviceable polynucleotide-acting enzymes are exemplifiednon-exclusively by enzymes with polynucleotide-cleaving activity,enzymes with polynucleotide-methylating activity, enzymes withpolynucleotide-ligating activity, and enzymes with a plurality ofdistinguishable enzymatic activities (including non-exclusively, e.g.,both polynucleotide-cleaving activity and polynucleotide-ligatingactivity).

Relevant polynucleotide-acting enzymes thus also include anycommercially available or non-commercially available polynucleotideendonucleases and their companion methylases including those cataloguedat the website http://www.neb.com/rebase, and those mentioned in thefollowing cited reference (Roberts and Macelis, 1996). Preferredpolynucleotide endonucleases include—but are not limited to—type IIrestriction enzymes (including type IIS), and include enzymes thatcleave both strands of a double stranded polynucleotide (e.g. Not I,which cleaves both strands at 5′ . . . GC/GGCCGC . . . 3′) and enzymesthat cleave only one strand of a double stranded polynucleotide, i.e.enzymes that have polynucleotide-nicking activity, (e.g. N. BstNB I,which cleaves only one strand at 5′ . . . GAGTCNNNN/N . . . 3′).Relevant polynucleotide-acting enzymes also include type III restrictionenzymes.

It is appreciated that relevant polynucleotide-acting enzymes alsoinclude any enzymes that may be developed in the future, thoughcurrently unavailable, that are serviceable for generating a ligationcompatible end, preferably a sticky end, in a polynucleotide.

In one preferred exemplification, a serviceable selection marker is arestriction site in a polynucleotide that allows a corresponding type II(or type IIS) restriction enzyme to cleave an end of the polynucleotideso as to provide a ligatable end (including a blunt end or alternativelya sticky end with at least a one base overhang) that is serviceable fora desirable ligation reaction without cleaving the polynucleotideinternally in a manner that destroys a desired internal sequence in thepolynucleotide. Thus it is provided that, among relevant restrictionsites, those sites that do not occur internally (i.e. that do not occurapart from the termini) in a specific working polynucleotide arepreferred when the use of a corresponding restriction enzyme(s) is notintended to cut the working polynucleotide internally. This allows oneto perform restriction digestion reactions to completion or to nearcompletion without incurring unwanted internal cleavage in a workingpolynucleotide.

According to a preferred aspect, it is thus preferable to userestriction sites that are not contained, or alternatively that are notexpected to be contained, or alternatively that unlikely to be contained(e.g. when sequence information regarding a working polynucleotide isincomplete) internally in a polynucleotide to be subjected toend-selection. In accordance with this aspect, it is appreciated thatrestriction sites that occur relatively infrequently are usuallypreferred over those that occur more frequently. On the other hand it isalso appreciated that there are occasions where internal cleavage of apolypeptide is desired, e.g. to achieve recombination or other mutagenicprocedures along with end-selection.

In accord with this invention, it is also appreciated that methods (e.g.mutagenesis methods) can be used to remove unwanted internal restrictionsites. It is also appreciated that a partial digestion reaction (i.e. adigestion reaction that proceeds to partial completion) can be used toachieve digestion at a recognition site in a terminal region whilesparing a susceptible restriction site that occurs internally in apolynucleotide and that is recognized by the same enzyme. In one aspect,partial digest are useful because it is appreciated that certain enzymesshow preferential cleavage of the same recognition sequence depending onthe location and environment in which the recognition sequence occurs.For example, it is appreciated that, while lambda DNA has 5 EcoR Isites, cleavage of the site nearest to the right terminus has beenreported to occur 10 times faster than the sites in the middle of themolecule. Also, for example, it has been reported that, while Sac II hasfour sites on lambda DNA, the three clustered centrally in lambda arecleaved 50 times faster than the remaining site near the terminus (atnucleotide 40,386). Summarily, site preferences have been reported forvarious enzymes by many investigators (e.g., Thomas and Davis, 1975;Forsblum et al, 1976; Nath and Azzolina, 1981; Brown and Smith, 1977;Gingeras and Brooks, 1983; Krüger et al, 1988; Conrad and Topal, 1989;Oller et al, 1991; Topal, 1991; and Pein, 1991; to name but a few). Itis appreciated that any empirical observations as well as anymechanistic understandings of site preferences by any serviceablepolynucleotide-acting enzymes, whether currently available or to beprocured in the future, may be serviceable in end-selection according tothis invention.

It is also appreciated that protection methods can be used toselectively protect specified restriction sites (e.g. internal sites)against unwanted digestion by enzymes that would otherwise cut a workingpolypeptide in response to the presence of those sites; and that suchprotection methods include modifications such as methylations and basesubstitutions (e.g. U instead of T) that inhibit an unwanted enzymeactivity. It is appreciated that there are limited numbers of availablerestriction enzymes that are rare enough (e.g. having very longrecognition sequences) to create large (e.g. megabase-long) restrictionfragments, and that protection approaches (e.g. by methylation) areserviceable for increasing the rarity of enzyme cleavage sites. The useof M.Fnu II (mCGCG) to increase the apparent rarity of Not Iapproximately twofold is but one example among many (Qiang et al, 1990;Nelson et al, 1984; Maxam and Gilbert, 1980; Raleigh and Wilson, 1986).

According to a preferred aspect of this invention, it is provided that,in general, the use of rare restriction sites is preferred. It isappreciated that, in general, the frequency of occurrence of arestriction site is determined by the number of nucleotides containedtherein, as well as by the ambiguity of the base requirements containedtherein. Thus, in a non-limiting exemplification, it is appreciatedthat, in general, a restriction site composed of, for example, 8specific nucleotides (e.g. the Not I site or GC/GGCCGC, with anestimated relative occurrence of 1 in 4⁸, i.e. 1 in 65,536, random8-mers) is relatively more infrequent than one composed of, for example,6 nucleotides (e.g. the Sma I site or CCC/GGG, having an estimatedrelative occurrence of 1 in 4⁶, i.e. 1 in 4,096, random ti-mers), whichin turn is relatively more infrequent than one composed of, for example,4 nucleotides (e.g. the Msp I site or C/CGG, having an estimatedrelative occurrence of 1 in 4⁴, i.e. 1 in 256, random 4-mers). Moreover,in another non-limiting exemplification, it is appreciated that, ingeneral, a restriction site having no ambiguous (but only specific) baserequirements (e.g. the Fin I site or GTCCC, having an estimated relativeoccurrence of 1 in 4⁵, i.e. 1 in 1024, random 5-mers) is relatively moreinfrequent than one having an ambiguous W (where W=A or T) baserequirement (e.g. the Ava II site or G/GWCC, having an estimatedrelative occurrence of 1 in 4×4×2×4×4—i.e. 1 in 512—random 5-mers),which in turn is relatively more infrequent than one having an ambiguousN (where N=A or C or G or T) base requirement (e.g. the Asu I site orG/GNCC, having an estimated relative occurrence of 1 in 4×4×1=4=4, i.e.1 in 256—random 5-mers). These relative occurrences are consideredgeneral estimates for actual polynucleotides, because it is appreciatedthat specific nucleotide bases (not to mention specific nucleotidesequences) occur with dissimilar frequencies in specificpolynucleotides, in specific species of organisms, and in specificgroupings of organisms. For example, it is appreciated that the % G+Ccontents of different species of organisms are often very different andwide ranging.

The use of relatively more infrequent restriction sites as a selectionmarker include—in a non-limiting fashion—preferably those sites composedat least a 4 nucleotide sequence, more preferably those composed atleast a 5 nucleotide sequence, more preferably still those composed atleast a 6 nucleotide sequence (e.g. the BamH I site or G/GATCC, the BglII site or A/GATCT, the Pst I site or CTGCA/G, and the Xba I site orT/CTAGA), more preferably still those composed at least a 7 nucleotidesequence, more preferably still those composed of an 8 nucleotidesequence nucleotide sequence (e.g. the Asc I site or GG/CGCGCC, the NotI site or GC/GGCCGC, the Pac I site or TTAAT/TAA, the Pme I site orGTTT/AAAC, the Srf I site or GCCC/GGGC, the Sse838 I site or CCTGCA/GG,and the Swa I site or ATTT/AAAT), more preferably still those composedof a 9 nucleotide sequence, and even more preferably still thosecomposed of at least a 10 nucleotide sequence (e.g. the BspG I site orCG/CGCTGGAC). It is further appreciated that some restriction sites(e.g. for class IIS enzymes) are comprised of a portion of relativelyhigh specificity (i.e. a portion containing a principal determinant ofthe frequency of occurrence of the restriction site) and a portion ofrelatively low specificity; and that a site of cleavage may or may notbe contained within a portion of relatively low specificity. Forexample, in the Eco57 I site or CTGAAG(16/14), there is a portion ofrelatively high specificity (i.e. the CTGAAG portion) and a portion ofrelatively low specificity (i.e. the N16 sequence) that contains a siteof cleavage.

In another preferred embodiment of this invention, a serviceableend-selection marker is a terminal sequence that is recognized by apolynucleotide-acting enzyme that recognizes a specific polynucleotidesequence. In a preferred aspect of this invention, serviceablepolynucleotide-acting enzymes also include other enzymes in addition toclassic type II restriction enzymes. According to this preferred aspectof this invention, serviceable polynucleotide-acting enzymes alsoinclude gyrases, helicases, recombinases, relaxases, and any enzymesrelated thereto.

Among preferred examples are topoisomerases (which have been categorizedby some as a subset of the gyrases) and any other enzymes that havepolynucleotide-cleaving activity (including preferablypolynucleotide-nicking activity) &/or polynucleotide-ligating activity.Among preferred topoisomerase enzymes are topoisomerase I enzymes, whichis available from many commercial sources (Epicentre Technologies,Madison, Wis.; Invitrogen, Carlsbad, Calif.; Life Technologies,Gaithersburg, Md.) and conceivably even more private sources. It isappreciated that similar enzymes may be developed in the future that areserviceable for end-selection as provided herein. A particularlypreferred topoisomerase I enzyme is a topoisomerase I enzyme of vacciniavirus origin, that has a specific recognition sequence (e.g. 5′ . . .AAGGG . . . 3′) and has both polynucleotide-nicking activity andpolynucleotide-ligating activity. Due to the specific nicking-activityof this enzyme (cleavage of one strand), internal recognition sites arenot prone to polynucleotide destruction resulting from the nickingactivity (but rather remain annealed) at a temperature that causesdenaturation of a terminal site that has been nicked. Thus for use inend-selection, it is preferable that a nicking site fortopoisomerase-based end-selection be no more than 100 nucleotides from aterminus, more preferably no more than 50 nucleotides from a terminus,more preferably still no more than 25 nucloetides from a terminus, evenmore preferably still no more than 20 nucleotides from a terminus, evenmore preferably still no more than 15 nucleotides from a terminus, evenmore preferably still no more than 10 nucleotides from a terminus, evenmore preferably still no more than 8 nucleotides from a terminus, evenmore preferably still no more than 6 nucleotides from a terminus, andeven more preferably still no more than 4 nucleotides from a terminus.

In a particularly preferred exemplification that is non-limiting yetclearly illustrative, it is appreciated that when a nicking site fortopoisomerase-based end-selection is 4 nucleotides from a terminus,nicking produces a single stranded oligo of 4 bases (in a terminalregion) that can be denatured from its complementary strand in anend-selectable polynucleotide; this provides a sticky end (comprised of4 bases) in a polynucleotide that is serviceable for an ensuing ligationreaction. To accomplish ligation to a cloning vector (preferably anexpression vector), compatible sticky ends can be generated in a cloningvector by any means including by restriction enzyme-based means. Theterminal nucleotides (comprised of 4 terminal bases in this specificexample) in an end-selectable polynucleotide terminus are thus wiselychosen to provide compatibility with a sticky end generated in a cloningvector to which the polynucleotide is to be ligated.

On the other hand, internal nicking of an end-selectable polynucleotide,e.g. 500 bases from a terminus, produces a single stranded oligo of 500bases that is not easily denatured from its complementary strand, butrather is serviceable for repair (e.g. by the same topoisomerase enzymethat produced the nick).

This invention thus provides a method—e.g. that is vacciniatopoisomerase-based &/or type II (or IIS) restriction endonuclease-based&/or type III restriction endonuclease-based &/or nicking enzyme-based(e.g. using N. BstNB I)—for producing a sticky end in a workingpolynucleotide, which end is ligation compatible, and which end can becomprised of at least a 1 base overhang. Preferably such a sticky end iscomprised of at least a 2-base overhang, more preferably such a stickyend is comprised of at least a 3-base overhang, more preferably stillsuch a sticky end is comprised of at least a 4-base overhang, even morepreferably still such a sticky end is comprised of at least a 5-baseoverhang, even more preferably still such a sticky end is comprised ofat least a 6-base overhang. Such a sticky end may also be comprised ofat least a 7-base overhang, or at least an 8-base overhang, or at leasta 9-base overhang, or at least a 10-base overhang, or at least 15-baseoverhang, or at least a 20-base overhang, or at least a 25-baseoverhang, or at least a 30-base overhang. These overhangs can becomprised of any bases, including A, C, G, or T.

It is appreciated that sticky end overhangs introduced usingtopoisomerase or a nicking enzyme (e.g. using N. BstNB I) can bedesigned to be unique in a ligation environment, so as to preventunwanted fragment reassemblies, such as self-dimerizations and otherunwanted concatamerizations.

According to one aspect of this invention, a plurality of sequences(which may but do not necessarily overlap) can be introduced into aterminal region of an end-selectable polynucleotide by the use of anoligo in a polymerase-based reaction. In a relevant, but by no meanslimiting example, such an oligo can be used to provide a preferred 5′terminal region that is serviceable for topoisomerase I-basedend-selection, which oligo is comprised of: a 1-10 base sequence that isconvertible into a sticky end (preferably by a vaccinia topoisomeraseI), a ribosome binding site (i.e. and “RBS”, that is preferablyserviceable for expression cloning), and optional linker sequencefollowed by an ATG start site and a template-specific sequence of 0-100bases (to facilitate annealment to the template in the apolymerase-based reaction). Thus, according to this example, aserviceable oligo (which may be termed a forward primer) can have thesequence: 5′ [terminal sequence=(N)₁₋₁₀] [topoisomerase I site &RBS=AAGGGAGGAG] [linker=(N)₁₋₁₀₀][start codon and template-specificsequence=ATG(N)₀₋₁₀₀]3′.

Analogously, in a relevant, but by no means limiting example, an oligocan be used to provide a preferred 3′ terminal region that isserviceable for topoisomerase I-based end-selection, which oligo iscomprised of: a 1-10 base sequence that is convertible into a sticky end(preferably by a vaccinia topoisomerase I), and optional linker sequencefollowed by a template-specific sequence of 0-100 bases (to facilitateannealment to the template in the a polymerase-based reaction). Thus,according to this example, a serviceable oligo (which may be termed areverse primer) can have the sequence: 5′ [terminal sequence=(N)₁₋₁₀][topoisomerase I site=AAGGG] [linker=(N)₁₋₁₀₀] [template-specificsequence=(N)₀₋₁₀₀]3′.

It is appreciated that, end-selection can be used to distinguish andseparate parental template molecules (e.g. to be subjected tomutagenesis) from progeny molecules (e.g. generated by mutagenesis). Forexample, a first set of primers, lacking in a topoisomerase Irecognition site, can be used to modify the terminal regions of theparental molecules (e.g. in polymerase-based amplification). A differentsecond set of primers (e.g. having a topoisomerase I recognition site)can then be used to generate mutated progeny molecules (e.g. using anypolynucleotide chimerization method, such as interrupted synthesis,template-switching polymerase-based amplification, or interruptedsynthesis; or using saturation mutagenesis; or using any other methodfor introducing a topoisomerase I recognition site into a mutagenizedprogeny molecule as disclosed herein) from the amplified templatemolecules. The use of topoisomerase I-based end-selection can thenfacilitate, not only discernment, but selective topoisomerase I-basedligation of the desired progeny molecules.

Annealment of a second set of primers to thusly amplified parentalmolecules can be facilitated by including sequences in a first set ofprimers (i.e. primers used for amplifying a set parental molecules) thatare similar to a toposiomerase I recognition site, yet different enoughto prevent functional toposiomerase I enzyme recognition. For example,sequences that diverge from the AAGGG site by anywhere from 1 base toall 5 bases can be incorporated into a first set of primers (to be usedfor amplifying the parental templates prior to subjection tomutagenesis). In a specific, but non-limiting aspect, it is thusprovided that a parental molecule can be amplified using the followingexemplary—but by no means limiting—set of forward and reverse primers:

Forward Primer: 5′ CTAGAAGAGAGGAGAAAACCATG(N)₁₀₋₁₀₀ 3′, andReverse Primer: 5′ GATCAAAGGCGCGCCTGCAGG(N)₁₀₋₁₀₀ 3′

According to this specific example of a first set of primers, (N)₁₀₋₁₀₀represents preferably a 10 to 100 nucleotide-long template-specificsequence, more preferably a 10 to 50 nucleotide-long template-specificsequence, more preferably still a 10 to 30 nucleotide-longtemplate-specific sequence, and even more preferably still a 15 to 25nucleotide-long template-specific sequence.

According to a specific, but non-limiting aspect, it is thus providedthat, after this amplification (using a disclosed first set of primerslacking in a true topoisomerase I recognition site), amplified parentalmolecules can then be subjected to mutagenesis using one or more sets offorward and reverse primers that do have a true topoisomerase Irecognition site. In a specific, but non-limiting aspect, it is thusprovided that a parental molecule can be used as templates for thegeneration of a mutagenized progeny molecule using the followingexemplary—but by no means limiting—second set of forward and reverseprimers:

Forward Primer: 5′ CTAGAAGGGAGGAGAAAACCATG 3′ Reverse Primer: 5′GATCAAAGGCGCGCCTGCAGG 3′ (contains Asc I recognition sequence)

It is appreciated that any number of different primers sets notspecifically mentioned can be used as first, second, or subsequent setsof primers for end-selection consistent with this invention. Notice thattype II restriction enzyme sites can be incorporated (e.g. an Asc I sitein the above example). It is provided that, in addition to the othersequences mentioned, the experimentalist can incorporate one or moreN,N,G/T triplets into a serviceable primer in order to subject a workingpolynucleotide to saturation mutagenesis. Summarily, use of a secondand/or subsequent set of primers can achieve dual goals of introducing atopoisomerase I site and of generating mutations in a progenypolynucleotide.

Thus, according to one use provided, a serviceable end-selection markeris an enzyme recognition site that allows an enzyme to cleave (includingnick) a polynucleotide at a specified site, to produce aligation-compatible end upon denaturation of a generated single strandedoligo. Ligation of the produced polynucleotide end can then beaccomplished by the same enzyme (e.g. in the case of vaccinia virustopoisomerase I), or alternatively with the use of a different enzyme.According to one aspect of this invention, any serviceable end-selectionmarkers, whether like (e.g. two vaccinia virus topoisomerase Irecognition sites) or unlike (e.g. a class II restriction enzymerecognition site and a vaccinia virus topoisomerase I recognition site)can be used in combination to select a polynucleotide. Each selectablepolynucleotide can thus have one or more end-selection markers, and theycan be like or unlike end-selection markers. In a particular aspect, aplurality of end-selection markers can be located on one end of apolynucleotide and can have overlapping sequences with each other.

It is important to emphasize that any number of enzymes, whethercurrently in existence or to be developed, can be serviceable inend-selection according to this invention. For example, in a particularaspect of this invention, a nicking enzyme (e.g. N. BstNB I, whichcleaves only one strand at 5′ . . . GAGTCNNNN/N . . . 3′) can be used inconjunction with a source of polynucleotide-ligating activity in orderto achieve end-selection. According to this embodiment, a recognitionsite for N. BstNB I—instead of a recognition site for topoisomeraseI—should be incorporated into an end-selectable polynucleotide (whetherend-selection is used for selection of a mutagenized progeny molecule orwhether end-selection is used apart from any mutagenesis procedure).

It is appreciated that the instantly disclosed end-selection approachusing topoisomerase-based nicking and ligation has several advantagesover previously available selection methods. In sum, this approachallows one to achieve direction cloning (including expression cloning).Specifically, this approach can be used for the achievement of: directligation (i.e. without subjection to a classicrestriction-purification-ligation reaction, that is susceptible to amultitude of potential problems from an initial restriction reaction toa ligation reaction dependent on the use of T4 DNA ligase); separationof progeny molecules from original template molecules (e.g. originaltemplate molecules lack topoisomerase I sites that not introduced untilafter mutagenesis), obviation of the need for size separation steps(e.g. by gel chromatography or by other electrophoretic means or by theuse of size-exclusion membranes), preservation of internal sequences(even when topoisomerase I sites are present), obviation of concernsabout unsuccessful ligation reactions (e.g. dependent on the use of T4DNA ligase, particularly in the presence of unwanted residualrestriction enzyme activity), and facilitated expression cloning(including obviation of frame shift concerns). Concerns about unwantedrestriction enzyme-based cleavages—especially at internal restrictionsites (or even at often unpredictable sites of unwanted star activity)in a working polynucleotide—that are potential sites of destruction of aworking polynucleotide can also be obviated by the instantly disclosedend-selection approach using topoisomerase-based nicking and ligation.

Two-Hybrid Based Screening Assays

Shuffling can also be used to recombinatorially diversify a pool ofselected library members obtained by screening a two-hybrid screeningsystem to identify library members which bind a predeterminedpolypeptide sequence. The selected library members are pooled andshuffled by in vitro and/or in vivo recombination. The shuffled pool canthen be screened in a yeast two hybrid system to select library memberswhich bind said predetermined polypeptide sequence (e.g., and SH2domain) or which bind an alternate predetermined polypeptide sequence(e.g., an SH2 domain from another protein species).

An approach to identifying polypeptide sequences which bind to apredetermined polypeptide sequence has been to use a so-called“two-hybrid” system wherein the predetermined polypeptide sequence ispresent in a fusion protein (Chien et al, 1991). This approachidentifies protein-protein interactions in vivo through reconstitutionof a transcriptional activator (Fields and Song, 1989), the yeast Ga14transcription protein. Typically, the method is based on the propertiesof the yeast Ga14 protein, which consists of separable domainsresponsible for DNA-binding and transcriptional activation.Polynucleotides encoding two hybrid proteins, one consisting of theyeast Ga14 DNA-binding domain fused to a polypeptide sequence of a knownprotein and the other consisting of the Ga14 activation domain fused toa polypeptide sequence of a second protein, are constructed andintroduced into a yeast host cell. Intermolecular binding between thetwo fusion proteins reconstitutes the Ga14 DNA-binding domain with theGal4 activation domain, which leads to the transcriptional activation ofa reporter gene (e.g., lacz, HIS3) which is operably linked to a Ga14binding site. Typically, the two-hybrid method is used to identify novelpolypeptide sequences which interact with a known protein (Silver andHunt, 1993; Durfee et al, 1993; Yang et al, 1992; Luban et al, 1993;Hardy et al, 1992; Bartel et al, 1993; and Vojtek et al, 1993). However,variations of the two-hybrid method have been used to identify mutationsof a known protein that affect its binding to a second known protein (Liand Fields, 1993; Lalo et al, 1993; Jackson et al, 1993; and Madura etal, 1993). Two-hybrid systems have also been used to identifyinteracting structural domains of two known proteins (Bardwell et al,1993; Chakrabarty et al, 1992; Staudinger et al, 1993; and Milne andWeaver 1993) or domains responsible for oligomerization of a singleprotein (Iwabuchi et al, 1993; Bogerd et al, 1993). Variations oftwo-hybrid systems have been used to study the in vivo activity of aproteolytic enzyme (Dasmahapatra et al, 1992). Alternatively, an E.coli/BCCP interactive screening system (Germino et al, 1993; Guarente,1993) can be used to identify interacting protein sequences (i.e.,protein sequences which heterodimerize or form higher orderheteromultimers). Sequences selected by a two-hybrid system can bepooled and shuffled and introduced into a two-hybrid system for one ormore subsequent rounds of screening to identify polypeptide sequenceswhich bind to the hybrid containing the predetermined binding sequence.The sequences thus identified can be compared to identify consensussequence(s) and consensus sequence kernals.

In general, standard techniques of recombination DNA technology aredescribed in various publications (e.g. Sambrook et al, 1989; Ausubel etal, 1987; and Berger and Kimmel, 1987; each of which is incorporatedherein in its entirety by reference. Polynucleotide modifying enzymeswere used according to the manufacturer's recommendations.Oligonucleotides were synthesized on an Applied Biosystems Inc. Model394 DNA synthesizer using ABI chemicals. If desired, PCR amplimers foramplifying a predetermined DNA sequence may be selected at thediscretion of the practitioner.

One microgram samples of template DNA are obtained and treated with U.V.light to cause the formation of dimers, including TT dimers,particularly purine dimers. U.V. exposure is limited so that only a fewphotoproducts are generated per gene on the template DNA sample.Multiple samples are treated with U.V. light for varying periods of timeto obtain template DNA samples with varying numbers of dimers from U.V.exposure.

A random priming kit which utilizes a non-proofreading polymease (forexample, Prime-It II Random Primer Labeling kit by Stratagene CloningSystems) is utilized to generate different size polynucleotides bypriming at random sites on templates which are prepared by U.V. light(as described above) and extending along the templates. The primingprotocols such as described in the Prime-It II Random Primer Labelingkit may be utilized to extend the primers. The dimers formed by U.V.exposure serve as a roadblock for the extension by the non-proofreadingpolymerase. Thus, a pool of random size polynucleotides is present afterextension with the random primers is finished.

The present invention is further directed to a method for generating aselected mutant polynucleotide sequence (or a population of selectedpolynucleotide sequences) typically in the form of amplified and/orcloned polynucleotides, whereby the selected polynucleotide sequences(s)possess at least one desired phenotypic characteristic (e.g., encodes apolypeptide, promotes transcription of linked polynucleotides, binds aprotein, and the like) which can be selected for. One method foridentifying hybrid polypeptides that possess a desired structure orfunctional property, such as binding to a predetermined biologicalmacromolecule (e.g., a receptor), involves the screening of a largelibrary of polypeptides for individual library members which possess thedesired structure or functional property conferred by the amino acidsequence of the polypeptide.

In one embodiment, the present invention provides a method forgenerating libraries of displayed polypeptides or displayed antibodiessuitable for affinity interaction screening or phenotypic screening. Themethod comprises (1) obtaining a first plurality of selected librarymembers comprising a displayed polypeptide or displayed antibody and anassociated polynucleotide encoding said displayed polypeptide ordisplayed antibody, and obtaining said associated polynucleotides orcopies thereof wherein said associated polynucleotides comprise a regionof substantially identical sequences, optimally introducing mutationsinto said polynucleotides or copies, (2) pooling the polynucleotides orcopies, (3) producing smaller or shorter polynucleotides by interruptinga random or particularized priming and synthesis process or anamplification process, and (4) performing amplification, preferably PCRamplification, and optionally mutagenesis to homologously recombine thenewly synthesized polynucleotides.

It is a particularly preferred object of the invention to provide aprocess for producing hybrid polynucleotides which express a usefulhybrid polypeptide by a series of steps comprising:

(a) producing polynucleotides by interrupting a polynucleotideamplification or synthesis process with a means for blocking orinterrupting the amplification or synthesis process and thus providing aplurality of smaller or shorter polynucleotides due to the replicationof the polynucleotide being in various stages of completion;(b) adding to the resultant population of single- or double-strandedpolynucleotides one or more single- or double-stranded oligonucleotides,wherein said added oligonucleotides comprise an area of identity in anarea of heterology to one or more of the single- or double-strandedpolynucleotides of the population;(c) denaturing the resulting single- or double-stranded oligonucleotidesto produce a mixture of single-stranded polynucleotides, optionallyseparating the shorter or smaller polynucleotides into pools ofpolynucleotides having various lengths and further optionally subjectingsaid polynucleotides to a PCR procedure to amplify one or moreoligonucleotides comprised by at least one of said polynucleotide pools;(d) incubating a plurality of said polynucleotides or at least one poolof said polynucleotides with a polymerase under conditions which resultin annealing of said single-stranded polynucleotides at regions ofidentity between the single-stranded polynucleotides and thus forming ofa mutagenized double-stranded polynucleotide chain;(e) optionally repeating steps (c) and (d);(f) expressing at least one hybrid polypeptide from said polynucleotidechain, or chains; and(g) screening said at least one hybrid polypeptide for a usefulactivity.

In a preferred aspect of the invention, the means for blocking orinterrupting the amplification or synthesis process is by utilization ofuv light, DNA adducts, DNA binding proteins.

In one embodiment of the invention, the DNA adducts, or polynucleotidescomprising the DNA adducts, are removed from the polynucleotides orpolynucleotide pool, such as by a process including heating the solutioncomprising the DNA fragments prior to further processing.

Having thus disclosed exemplary embodiments of the present invention, itshould be noted by those skilled in the art that the disclosures areexemplary only and that various other alternatives, adaptations andmodifications may be made within the scope of the present invention.Accordingly, the present invention is not limited to the specificembodiments as illustrated herein.

Without further elaboration, it is believed that one skilled in the artcan, using the preceding description, utilize the present invention toits fullest extent. The following examples are to be consideredillustrative and thus are not limiting of the remainder of thedisclosure in any way whatsoever.

Example 1 Generation of Random Size Polynucleotides Using U.V. InducedPhotoproducts

One microgram samples of template DNA are obtained and treated with U.V.light to cause the formation of dimers, including TT dimers,particularly purine dimers. U.V. exposure is limited so that only a fewphotoproducts are generated per gene on the template DNA sample.Multiple samples are treated with U.V. light for varying periods of timeto obtain template DNA samples with varying numbers of dimers from U.V.exposure.

A random priming kit which utilizes a non-proofreading polymerase (forexample, Prime-It II Random Primer Labeling kit by Stratagene CloningSystems) is utilized to generate different size polynucleotides bypriming at random sites on templates which are prepared by U.V. light(as described above) and extending along the templates. The primingprotocols such as described in the Prime-It II Random Primer Labelingkit may be utilized to extend the primers. The dimers formed by U.V.exposure serve as a roadblock for the extension by the non-proofreadingpolymerase. Thus, a pool of random size polynucleotides is present afterextension with the random primers is finished.

Example 2 Isolation of Random Size Polynucleotides

Polynucleotides of interest which are generated according to Example 1are gel isolated on a 1.5% agarose gel. Polynucleotides in the 100-300bp range are cut out of the gel and 3 volumes of 6 M Nal is added to thegel slice. The mixture is incubated at 50° C. for 10 minutes and 10 μlof glass milk (Bio 101) is added. The mixture is spun for 1 minute andthe supernatant is decanted. The pellet is washed with 500 μl of ColumnWash (Column Wash is 50% ethanol, 10 mM Tris-HCl pH 7.5, 100 mM NaCl and2.5 mM EDTA) and spin for 1 minute, after which the supernatant isdecanted. The washing, spinning and decanting steps are then repeated.The glass milk pellet is resuspended in 20 μl of H₂O and spun for 1minute. DNA remains in the aqueous phase.

Example 3 Shuffling of Isolated Random Size 100-300 bp Polynucleotides

The 100-300 bp polynucleotides obtained in Example 2 are recombined inan annealing mixture (0.2 mM each dNTP, 2.2 mM MgCl₂, 50 mM KCl, 10 mMTris-HCl ph 8.8, 0.1% Triton X-100, 0.3μ; Taq DNA polymerase, 50 μltotal volume) without adding primers. A Robocycler by Stratagene wasused for the annealing step with the following program: 95° C. for 30seconds, 25-50 cycles of [95° C. for 30 seconds, 50-60° C. (preferably58° C.) for 30 seconds, and 72° C. for 30 seconds] and 5 minutes at 72°C. Thus, the 100-300 bp polynucleotides combine to yield double-strandedpolynucleotides having a longer sequence. After separating out thereassembled double-stranded polynucleotides and denaturing them to formsingle stranded polynucleotides, the cycling is optionally againrepeated with some samples utilizing the single strands as template andprimer DNA and other samples utilizing random primers in addition to thesingle strands.

Example 4 Screening of Polypeptides from Shuffled Polynucleotides

The polynucleotides of Example 3 are separated and polypeptides areexpressed therefrom. The original template DNA is utilized as acomparative control by obtaining comparative polypeptides therefrom. Thepolypeptides obtained from the shuffled polynucleotides of Example 3 arescreened for the activity of the polypeptides obtained from the originaltemplate and compared with the activity levels of the control. Theshuffled polynucleotides coding for interesting polypeptides discoveredduring screening are compared further for secondary desirable traits.Some shuffled polynucleotides corresponding to less interesting screenedpolypeptides are subjected to reshuffling.

Example 5 Directed Evolution an Enzyme by Saturation Mutagenesis

Site-Saturation Mutagenesis: To accomplish site-saturation mutagenesisevery residue (316) of a dehalogenase enzyme was converted into all 20amino acids by site directed mutagenesis using 32-fold degenerateoligonucleotide primers, as follows:

1. A culture of the dehalogenase expression construct was grown and apreparation of the plasmid was made2. Primers were made to randomize each codon—they have the commonstructure X₂₀NN(G/T)X₂₀3. A reaction mix of 25 ul was prepared containing ˜50 ng of plasmidtemplate, 125 ng of each primer, 1× native Pfu buffer, 200 uM each dNTPand 2.5 U native Pfu DNA polymerase4. The reaction was cycled in a Robo96 Gradient Cycler as follows:Initial denaturation at 95° C. for 1 min 20 cycles of 95° C. for 45 sec,53° C. for 1 min and 72° C. for 11 min Final elongation step of 72° C.for 10 min5. The reaction mix was digested with 10 U of DpnI at 37° C. for 1 hourto digest the methylated template DNA6. Two ul of the reaction mix were used to transform 50 ul of XL1-BlueMRF′ cells and the entire transformation mix was plated on a largeLB-Amp-Met plate yielding 200-1000 colonies7. Individual colonies were toothpicked into the wells of 96-wellmicrotiter plates containing LB-Amp-IPTG and grown overnight8. The clones on these plates were assayed the following day

Screening:

Approximately 200 clones of mutants for each position were grown inliquid media (384 well microtiter plates) and screened as follows:

1. Overnight cultures in 384-well plates were centrifuged and the mediaremoved. To each well was added 0.06 mL 1 mM Tris/SO₄ ²⁻ pH 7.8.2. Made 2 assay plates from each parent growth plate consisting of 0.02mL cell suspension.3. One assay plate was placed at room temperature and the other atelevated temperature (initial screen used 55° C.) for a period of time(initially 30 minutes).4. After the prescribed time 0.08 mL room temperature substrate (TCPsaturated 1 mM Tris/SO₄ ²⁻ pH 7.8 with 1.5 mM NaN₃ and 0.1 mMbromothymol blue) was added to each well.5. Measurements at 620 nm were taken at various time points to generatea progress curve for each well.6. Data were analyzed and the kinetics of the cells heated to those notheated were compared. Each plate contained 1-2 columns (24 wells) ofunmutated 20F12 controls.7. Wells that appeared to have improved stability were re-grown andtested under the same conditions.

Following this procedure nine single site mutations appeared to conferincreased thermal stability on the enzyme. Sequence analysis wasperformed to determine of the exact amino acid changes at each positionthat were specifically responsible for the improvement. In sum, theimprovement was conferred at 7 sites by one amino acid change alone, atan eighth site by each of two amino acid changes, and at a ninth site byeach of three amino acid changes. Several mutants were then made eachhaving a plurality of these nine beneficial site mutations incombination; of these two mutants proved superior to all the othermutants, including those with single point mutations.

Example 6 Direct Expression Cloning Using End-Selection

An esterase gene was amplified using 5′phosphorylated primers in astandard PCR reaction (10 ng template; PCR conditions: 3′ 94 C; [1′ 94C; 1′ 50 C; 1′30″ 68 C]×30; 10′ 68 C.

Forward Primer = 9511TopF (CTAGAAGGGAGGAGAATTACATGAAGCGGCTTTTAGCCC)Reverse Primer = 9511TopR (AGCTAAGGGTCAAGGCCGCACCCGAGG)The resulting PCR product (ca.1000 bp) was gel purified and quantified.

A vector for expression cloning, pASK3 (Institut fuer Bioanalytik,Goettingen, Germany), was cut with Xba I and Bgl II and dephosphorylatedwith CIP.

0.5 pmoles Vaccina Topoisomerase I (Invitrogen, Carlsbad, Calif.) wasadded to 60 ng (ca. 0.1 pmole) purified PCR product for 5′ 37 C inbuffer NEB I (New England Biolabs, Beverly, Mass.) in 5 μl total volume.

The topogated PCR product was cloned into the vector pASK3 (5 ca. 200 ngin NEB I) for 5′ at room temperature.

This mixture was dialyzed against H₂O for 30′. 2 μl were used forelectroporation of DH10B cells (Gibco BRL, Gaithersburg, Md.).

Efficiency: Based on the actual clone numbers this method can produce2×10⁶ clones per μg vector. All tested recombinants showed esteraseactivity after induction with anhydrotetracycline.

Example 7 Dehalogenase Thermal Stability

This invention provides that a desirable property to be generated bydirected evolution is exemplified in a limiting fashion by an improvedresidual activity (e.g. an enzymatic activity, an immunoreactivity, anantibiotic acivity, etc.) of a molecule upon subjection to alteredenvironment, including what may be considered a harsh enviroment, for aspecified time. Such a harsh environment may comprise any combination ofthe following (iteratively or not, and in any order or permutation): anelevated temperature (including a temperature that may causedenaturation of a working enzyme), a decreased temperature, an elevatedsalinity, a decreased salinity, an elevated pH, a decreased pH, anelevated pressure, a decreassed pressure, and an change in exposure to aradiation source (including uv radiation, visible light, as well as theentire electromagnetic spectrum).

The following example shows an application of directed evolution toevolve the ability of an enzyme to regain &/or retain activity uponexposure to an elevated temperature.

Every residue (316) of a dehalogenase enzyme was converted into all 20amino acids by site directed mutagenesis using 32-fold degenerateoligonucleotide primers. These mutations were introduced into thealready rate-improved variant Dhla 20F12. Approximately 200 clones ofeach position were grown in liquid media (384 well microtiter plates) tobe screened. The screening procedure was as follows:

1. Overnight cultures in 384-well plates were centrifuged and the mediaremoved. To each well was added 0.06 mL 1 mM Tris/SO₄ ²⁻ pH 7.8.2. The robot made 2 assay plates from each parent growth plateconsisting of 0.02 mL cell suspension.3. One assay plate was placed at room temperature and the other atelevated temperature (initial screen used 55° C.) for a period of time(initially 30 minutes).4. After the prescribed time 0.08 mL room temperature substrate (TCPsaturated 1 mM Tris/SO₄ ²⁻ pH 7.8 with 1.5 mM NaN₃ and 0.1 mMbromothymol blue) was added to each well. TCP=trichloropropane.5. Measurements at 620 nm were taken at various time points to generatea progress curve for each well.6. Data were analyzed and the kinetics of the cells heated to those notheated were compared. Each plate contained 1-2 columns (24 wells) ofun-mutated 20F12 controls.7. Wells that appeared to have improved stability were regrown andtested under the same conditions.

Following this procedure nine single site mutations appeared to conferincreased thermal stability on Dhla-20F12. Sequence analysis showed thatthe following changes were beneficial:

D89G F91S T159L G189Q, G189V 1220L N238T W251Y P302A, P302L, P302S,P302K P302R/S306R

Only two sites (189 and 302) had more than one substitution. The first 5on the list were combined (using G189Q) into a single gene (this mutantis referred to as “Dhla5”). All changes but S306R were incorporated intoanother variant referred to as Dhla8.

Thermal stability was assessed by incubating the enzyme at the elevatedtemperature (55° C. and 80° C.) for some period of time and activityassay at 30° C. Initial rates were plotted vs. time at the highertemperature. The enzyme was in 50 mM Tris/SO₄ pH 7.8 for both theincubation and the assay. Product (Cl⁻) was detected by a standardmethod using Fe(NO₃)₃ and HgSCN. Dhla 20F12 was used as the de factowild type. The apparent half-life (T_(1/2)) was calculated by fittingthe data to an exponential decay function.

According to another aspect of this invention, ligation reassembly canbe performed using a solid support. The following example 8(corresponding to FIG. 17) is illustrative but non-limiting.

Example 8 Solid Phase Gene Family Reassembly Protocol

The objective can be, e.g., to reassemble/shuffle molecules of DNA togenerate gene libraries of specific genes, libraries of gene families,and libraries of unrelated genes. The synthesis of the full-lengthmolecules is carried out on a solid support. As solid support we useparamagnetic beads coated with Streptavidin. The principle is based onthe strong interaction between Biotin and Streptavidin and the abilityto stepwise or simulataneously ligate DNA fragments generated from theannealing of nucleic acid building blocks (such as ssDNA buildingblocks). The use of a solid support facilitates the reassembly ofnucleic acid building blocks in a sequential manner and thus allows oneto use not only unique couplings, but also redundant or repeatedcouplings throughout the length of a nucleic acid molecule that is to begenerated by ligation reassembly.

A “capture oligonucleotide” is biotinylated at the 5′end for binding tothe beads. The “capture oligo” is annealed to a complementary sequence(no biotinylated). The double stranded capture fragment contains tworestriction sites at the 5′-end which allows release of the assembledmolecules from the solid support.

Ligation reassembly is performed by step-wise ligation of annealedoligonucleotides of 20-100 bases. The first fragment of the assemblycontains a 5′-end compatible with the 3′-end of the capture biotinylatedfragment. Consecutive ligation of double stranded fragments containingcomplementary ends allows the generation of full-length molecules. Halfway synthesis (midpoint) molecules are released from the solid support.A final ligation step between molecules generated from both ends resultsin the generation a full-length reassembled DNA.

Materials and Methods:

Streptavidin coated magnetic beads M280 (Dynal corp.)

Magnetic stand or magnetic particle concentrator (MPC stand)

Biotinylated capture oligos containing a 7 or 15 atom-spacer and tworestriction sites not internally found in the sequences beingreassembled. Ensure that the biotinylated capture oligo does not containfree biotin.

Design capture oligos to allow reassembly from both ends of thesequences being reassembled.

Design internal oligos according to the sequence (s) being reassembled

STE buffer

Washing/Binding buffer (1M NaCl, 10 mM Tris-HCl pH 7.5, 1 mM EDTA) PBS,pH 7.4 buffer containing 0.1% BSA.

Annealing/ligation buffer

Spin columns for DNA purification

1) Anneal equimolar amounts of complementary oligos by heating at 90° C.and slowly cooling down to room temperature in STE buffer. Diluteannealed oligos to 5 pmole/ul.2) Aliquot 300-ug of 10 mg/ml bead suspension in a 500 ul Eppendorftube.3) Wash the beads with 300-ul of PBS buffer using a magnetic stand.Repeat 3 times.4) Wash the beads with 300-ul of 1× Washing/Binding buffer using amagnetic stand. Repeat once.5) Immobilize the pre-annealed biotinylated capture fragments to thebeads (55 pmole of 500-bp dsDNA binds to 1 mg of beads). The bindingcapacity of the beads is fragment length dependent. Mix beads andcapture fragment in binding buffer. Incubate at room temperature for 12hin a 360 degree rotator6) Wash the beads with 300-ul of 60° C. pre-heated 1× Washing/bindingbuffer using. Repeat 3 times.7) Wash the beads with 300-ul of freshly thawed 1× ligation buffer.8) For a reassembly of “n” (5′ to 3′ and 3′ to 5′) fragments:

Mix: Fragment #1 (or “n”) (5 pmole) 10 ul 5 x ligase buffer 60 ul 1 U/ulT4 Ligase 15 ul dH₂O 215 ul 300 ul9) Incubate with rotation at RT for 30 min.10) Wash the beads with 300-ul of 60° C. pre-heated 1× Washing/Bindingbuffer. Repeat 3 times.11) Wash the beads with 300-ul of freshly thawed 1× ligation buffer.

12) Add:

Fragment #2 (n − 1)(5 pmole) 10 ul 5 x ligase buffer 60 ul 1 U/ul T4Ligase 15 ul dH₂O 215 ul 300 ul13) Incubate with rotation at RT for 30 min.14) Wash the beads with 300-ul of 60° C. pre-heated 1× Washing/bindingbuffer. Repeat 3 times.15) Wash the beads with 300-ul of freshly thawed 1× ligation buffer.16) Repeat the procedure until n/2 fragments have been added from eachend of the synthesis17) Elute the partially assembled products from the solid support bycutting with the corresponding restriction enzyme

Beads with immobilized reassembled gene x ul 10 x enzyme buffer 30 ul 1U/ul restriction enzyme 5 ul dH₂O to 300 ul18) Replace restriction buffer of eluted DNA for ligation buffer using aspin column. Elute from spin column with H₂O19) Ligate both partially assembled products to generate reassembledfull-length molecules

partial synthesis product (5′ to 3′) 60 ul partial synthesis product (3′to 5′) 60 ul 5x ligase buffer 20 ul 1 U/ul T4 ligase 10 ul dH2O 50 ul200 ul20) Clone full-length genes in corresponding vector.21) Sequence a few clones and screen for different kinetic parameters ofthe expressed enzymes.

LITERATURE CITED

Unless otherwise indicated, all references cited herein (supra andinfra) are incorporated by reference in their entirety.

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What is claimed is:
 1. A method of non-stochastically producing alibrary of chimeric nucleic acid molecules having an overall assemblyorder that is non-random comprising: (a) non-randomly generating aplurality of nucleic acid building blocks having mutually compatibleligatable ends; and (b) assembling the nucleic acid building blocks,such that a designed overall assembly order is achieved; whereby a setof progenitor templates can be shuffled to generate a library of progenypolynucleotide molecules and correspondingly encoded polypeptides, andwhereby screening of the progeny polynucleotide library provides a meansto identify a desirable species that have a desirable property.
 2. Amethod of non-stochastically producing a library comprised of a definednumber of groupings comprised of one or more groupings of chimericnucleic acid molecules having an overall assembly order that is chosenby design, said method comprised of: (a) generating by design for eachgrouping a set of specific nucleic acid building blocks havingserviceable mutually compatible ligatable ends, and (b) assembling thesenucleic acid building blocks according to said groupings, such that adesigned overall assembly order is achieved; whereby a set of progenitortemplates can be shuffled to generate a library of progenypolynucleotide molecules and correspondingly encoded polypeptides, andwhereby the expression screening of the progeny polynucleotide libraryprovides a means to identify a desirable species that has a desirableproperty.